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fix-issues

Orchestrate a batch bug-fixing sprint. Supports scheduling with every/now/next/stop. Use sync to update trackers and verify/close already-fixed issues. Use plan to draft plans for skipped issues. Usage: /fix-issues N [focus] [auto] [every SCHEDULE] [now] | sync | plan [auto] | stop | next.

Run Skill in Manus

Overview

Install command

npx skills add https://github.com/zeveck/zskills --skill fix-issues

Copy and paste this command into Claude Code to install the skill

Source

zeveck/zskills

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UpdatedApril 18, 2026 at 02:40

SKILL.md

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/fix-issues N [focus] [auto] [every SCHEDULE] [now] | sync | plan [auto] | stop | next — Batch Bug-Fixing Sprint

Orchestrates large-scale bug fixing. Syncs trackers, prioritizes issues, dispatches agent teams in worktrees, verifies fixes, writes a persistent report, and optionally auto-lands to main. Can self-schedule for recurring runs.

Ultrathink throughout. Use careful, thorough reasoning at every step.

Arguments

/fix-issues N [focus] [auto] [every SCHEDULE] [now]
/fix-issues sync | plan [auto] | stop | next

N (required for sprints) — number of issues to fix (e.g., 30)
focus (optional) — prioritize a specific domain. The agent scans plans/*_ISSUES.md and plans/ISSUES_PLAN.md to discover tracker files and their domains. Common focus values: new, correctness, codegen, ui, tests — but any domain found in your tracker files works. Omit for default priority order.
auto (optional) — bypass confirmation gates for autonomous operation. Behavior depends on context:
- Sprints: skip Phase 2 issue list approval, auto-land to main via cherry-pick. Does NOT close GH issues or remove worktrees — those are /fix-report actions.
- plan auto: draft plans for all found issues without selection (see Plan section).
- Not applicable to sync. sync is always interactive — closing issues on GitHub requires human approval.
every SCHEDULE (optional) — self-schedule recurring runs via cron:
- Accepts intervals: 4h, 2h, 30m, 12h
- Accepts time-of-day: day at 9am, day at 14:00, weekday at 9am
- Without now: schedules only, does NOT run immediately
- With now: schedules AND runs immediately
- Implies auto — scheduling only makes sense for autonomous runs
- Each run re-registers the cron (self-perpetuating)
- Cron is session-scoped — dies when the session dies
now (optional) — run immediately. When combined with every, runs immediately AND schedules. Without every, now is the default behavior (bare invocation always runs immediately).
sync — update all issue tracker files from GitHub, research new issues, AND verify/close issues that appear already fixed. Dispatches research agents that also check if open issues are already resolved in the codebase. Always interactive — presents findings and asks before closing. See Sync section for the full flow.
plan — draft plans for issues previously skipped as "too complex." Scans SPRINT_REPORT.md for skipped items, dispatches /draft-plan for each. No fixing — just creates plans for /run-plan to execute later.
stop — cancel any existing /fix-issues cron and exit. Takes precedence over all other arguments.
next — check when the next scheduled run will fire. Takes precedence over all other arguments except stop.
pr (optional) — land each fixed issue via a per-issue PR on a named branch (fix/issue-NNN) in a dedicated worktree. Overrides the config default execution.landing.
direct (optional) — land each fixed issue directly on main (no worktree isolation, no PR). Overrides the config default. Incompatible with execution.main_protected: true.

Detection: scan $ARGUMENTS for:

stop (case-insensitive) — cancel cron and exit (highest precedence)
next (case-insensitive) — check schedule and exit
sync (case-insensitive) — sync trackers, verify/close fixed issues, and exit
plan (case-insensitive) — draft plans for skipped issues and exit
now (case-insensitive) — run immediately
auto (case-insensitive) — autonomous mode (behavior varies by context)
every followed by a schedule expression — scheduling mode
pr (case-insensitive) — PR landing mode (per-issue branches + PRs)
direct (case-insensitive) — direct landing mode (commit on main)

Landing mode resolution (same pattern as /run-plan):

Explicit argument wins: pr or direct in $ARGUMENTS
Config default: read .claude/zskills-config.json execution.landing field
Fallback: cherry-pick

# Detect landing mode (same logic as /run-plan)
LANDING_MODE="cherry-pick"
if [[ "$ARGUMENTS" =~ (^|[[:space:]])[pP][rR]($|[[:space:]]) ]]; then
  LANDING_MODE="pr"
elif [[ "$ARGUMENTS" =~ (^|[[:space:]])[dD][iI][rR][eE][cC][tT]($|[[:space:]]) ]]; then
  LANDING_MODE="direct"
else
  CONFIG_FILE="$PROJECT_ROOT/.claude/zskills-config.json"
  if [ -f "$CONFIG_FILE" ]; then
    CONFIG_CONTENT=$(cat "$CONFIG_FILE")
    if [[ "$CONFIG_CONTENT" =~ \"landing\"[[:space:]]*:[[:space:]]*\"([^\"]*)\" ]]; then
      CFG_LANDING="${BASH_REMATCH[1]}"
      [ -n "$CFG_LANDING" ] && LANDING_MODE="$CFG_LANDING"
    fi
  fi
fi

# Validation: direct + main_protected -> error
if [[ "$LANDING_MODE" == "direct" ]]; then
  CONFIG_FILE="$PROJECT_ROOT/.claude/zskills-config.json"
  if [ -f "$CONFIG_FILE" ]; then
    CONFIG_CONTENT=$(cat "$CONFIG_FILE")
    if [[ "$CONFIG_CONTENT" =~ \"main_protected\"[[:space:]]*:[[:space:]]*true ]]; then
      echo "ERROR: direct mode is incompatible with main_protected: true. Use pr mode or change config."
      exit 1
    fi
  fi
fi

Strip pr/direct from arguments before parsing issue numbers, focus, or other tokens (same pattern as stripping auto, now, etc.). The downstream N/focus parser must not see pr or direct as an issue count or domain name.

Examples:

/fix-issues 30 — interactive, 30 issues, run now
/fix-issues 10 correctness — interactive, solver focus, run now
/fix-issues 5 auto — autonomous, one-time, run now
/fix-issues 5 auto every 4h — schedule every 4h (first run in ~4h)
/fix-issues 5 auto every 4h now — schedule every 4h + run immediately
/fix-issues 10 auto every day at 9am — schedule daily at 9am
/fix-issues 10 auto every weekday at 9am now — schedule + run now
/fix-issues sync — update trackers + verify/close fixed issues (always interactive)
/fix-issues plan — draft plans for issues skipped as "too complex"
/fix-issues plan auto — same, but plan all without selection
/fix-issues stop — cancel the recurring cron
/fix-issues next — check when the next sprint will run
/fix-issues 5 auto pr — autonomous sprint, per-issue PR landing
/fix-issues 3 auto direct — autonomous sprint, land commits on main directly

Now (standalone — no N provided)

If $ARGUMENTS is just now (no N, no focus, no every — just the word now by itself):

Use CronList to list all cron jobs
Find any whose prompt starts with Run /fix-issues
If found: extract the cron's prompt to get N, focus, auto, and schedule. Run the sprint immediately using those parameters — proceed to Phase 1 with the cron's N, focus, and auto settings. Do NOT ask for confirmation — now IS the confirmation. The cron itself stays active.
If none found: report No active /fix-issues cron to trigger. Use /fix-issues N to run manually. and exit.

Next (if `next` is present)

If $ARGUMENTS contains next (case-insensitive):

Use CronList to list all cron jobs
Find any whose prompt starts with Run /fix-issues
Report:
- If found: parse the cron expression and compute the next fire time. Use date +%Z for the timezone. Show both relative and absolute:
  
  Next fix-issues sprint in ~2h 15m (~8:30 PM ET, cron XXXX). Prompt: Run /fix-issues 5 auto every 4h
- If none found: No active /fix-issues cron in this session.
Exit. Do not proceed to any phase.

Stop (if `stop` is present)

If $ARGUMENTS contains stop (case-insensitive):

Use CronList to list all cron jobs
Delete ALL whose prompt starts with Run /fix-issues using CronDelete
Report what was cancelled:
- If one cron found: Fix-issues cron stopped (was job ID XXXX, every INTERVAL).
- If multiple found: Stopped N fix-issues crons (IDs: XXXX, YYYY).
- If none found: No active /fix-issues cron found.
Exit. Do not proceed to any phase. The stop command does nothing else.

Sync (if `sync` is present)

Update all issue trackers from GitHub, research new issues, and verify/close issues that appear already fixed. This is the single command for issue hygiene — it both syncs state AND cleans up resolved issues in one pass.

Always interactive. Closing issues on GitHub requires human approval — there is no auto mode for sync. The agent presents verified-fixed candidates and waits for the user to select which to close.

Step 1 — Fetch & update trackers

Run Phase 1a (Preflight & Sync) — fetch all open issues, run sync script, update all tracker files.

Step 2 — Research & verify

Before dispatching any Agent: check agents.min_model in .claude/zskills-config.json. If set, use that model or higher (ordinal: haiku=1 < sonnet=2 < opus=3). Never dispatch with a lower-ordinal model than the configured minimum.

Dispatch research agents for every open issue that lacks a research blurb in its tracker file. Each agent does:

Read the full issue body and comments from GitHub
Grep the codebase for related files and code
Write a concise research blurb (what's wrong, where, suggested approach)
Add the blurb to the appropriate tracker file

Additionally, each agent checks whether the issue appears to already be fixed in the codebase. This is the same pass — not a separate step. While researching an issue, the agent naturally reads the relevant code and can tell if the reported problem still exists. For each issue, the agent produces a verdict:

FIXED — code fix is present AND tests pass. Include: commit hash, what changed, which tests cover it.
LIKELY FIXED — code fix appears present but no specific tests cover this exact issue. Include what was found and what's missing.
NOT FIXED — the reported problem still exists in the code (normal — this is just a research blurb, the issue stays open).
UNCLEAR — can't determine from code review alone (needs manual testing).

Criteria for FIXED/LIKELY FIXED verdicts:

The specific code the issue reported as broken has been changed
Tests exist that cover the reported behavior (FIXED) or not (LIKELY FIXED)
The fix commit references the issue number or is clearly related
Do NOT verdict as FIXED if: the issue is a feature request (not a bug), the fix is partial, or you're not confident

Also scan for additional close candidates from:

Tracker files — [x] items that are still open on GitHub
Sprint reports — entries in "Already Implemented" or "Already Fixed on Main" sections of SPRINT_REPORT.md

For these candidates, dispatch verification agents with the same checklist above (read issue body, check code, check tests, produce verdict).

Step 3 — Present findings

Show the sync summary and any close candidates:

Sync complete. N open issues, M newly researched, K tracker files updated.
Gaps: [any GH issues not in any tracker]

Issues that appear already fixed (N candidates):

| # | Title | Verdict | Evidence |
|---|-------|---------|----------|
| #126 | Fcn block mapping | FIXED | SlxImporter.js:85, commit abc1234, 2 tests |
| #191 | Block stubs | FIXED | All 4 blocks implemented, 12 tests pass |
| #393 | Fcn codegen u(N) | FIXED | codegen emitter step 8, commit def5678 |
| #200 | Some bug | LIKELY FIXED | Code changed but no regression test |

Close 3 FIXED issues? (all / comma-separated numbers / none)

Wait for user selection. LIKELY FIXED and UNCLEAR items are shown for context but NOT offered for closing — they need human judgment.
If no close candidates found: skip this step, just show the sync summary.

Step 4 — Close approved issues on GitHub

For each approved issue:

Close with a comment explaining what fixed it:

gh issue close <N> --comment "Fixed in commit <hash>. <brief description of fix>. Tests: <test file(s)>."

Update tracker files — mark the issue [x] in all relevant trackers.
Update SPRINT_REPORT.md — if the issue appears in an "Already Implemented" section, add a note: Closed by /fix-issues sync.

Step 5 — Commit & report

Commit updated tracker files.

Report:

Sync complete.
  Open issues: N
  Newly researched: M
  Tracker files updated: K
  Closed (verified fixed): J (#NNN, #NNN, ...)
  Likely fixed (needs human review): L (#NNN, #NNN)
  Gaps: [any GH issues not in any tracker]

Exit.

Plan (if `plan` is present)

Draft plans for issues previously skipped as "too complex for batch fix." Accepts optional auto — /fix-issues plan auto skips the selection gate and drafts plans for all found issues.

Run node scripts/skipped-issues.cjs --check-gh — this scans the ENTIRE SPRINT_REPORT.md across all sprints, extracts skipped issue numbers (including ranges like #148-#168), deduplicates against existing executable plans in plans/, and checks GitHub issue state. Output is JSON with each issue classified as needs-plan, has-plan, or closed.

Use the script output directly — do NOT manually grep SPRINT_REPORT.md.
Deduplicate — check plans/ for existing plans that already cover each issue. Also check whether the issue is still open on GitHub (gh issue view <N> --json state). Remove issues that already have a plan or are closed.

Present findings (unless auto):

Found N issues needing plans:

# Title Source
#142 Drag into subsystem Sprint 2026-03-17: Skipped — Too Complex
#363 Algebraic loop detection Sprint 2026-03-16: Remaining Open
...
Already have plans: #NNN, #NNN (skipped)
Already closed: #NNN (skipped)

Which issues should I draft plans for? (all / comma-separated numbers / none)

Wait for the user's selection before proceeding. If auto, skip this step and plan all of them.

For each selected issue, create a delegation requirement marker and then dispatch /draft-plan. The marker goes under fix-issues' own per-sprint subdir ($PIPELINE_ID) — the parent reconciles child fulfillment in its own scope:
```
MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
mkdir -p "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID"
printf 'skill: draft-plan\nparent: fix-issues\nissue: %s\ndate: %s\n' \
  "$ISSUE_NUMBER" "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/requires.draft-plan.$ISSUE_NUMBER"
```
Then dispatch /draft-plan with:
- The issue number and full body (gh issue view <N> --json body)
- Any research blurb from the tracker files
- Output path: plans/{issue-slug}.md
Report:
Plans drafted: N
- plans/foo-bar.md (#123) — [one-line summary]
- plans/baz-qux.md (#456) — [one-line summary] Already had plans: M (skipped) Closed issues: K (skipped) User declined: J
Exit. Plans are ready for /run-plan execution.

Phase 0 — Schedule (if `every` is present)

If $ARGUMENTS contains every <schedule>:

Parse the schedule — convert to a cron expression. The LLM interprets natural scheduling expressions.

For interval-based schedules (4h, 2h, 30m): use the CURRENT minute as the offset so the first fire is a full interval from now, not aligned to midnight. Check the current minute with date +%M:
- 4h at minute 9 → 9 */4 * * * (fires at :09 past every 4th hour)
- 2h at minute 15 → 15 */2 * * *
- 30m → */30 * * * * (no offset needed for sub-hour)
- 1h at minute 9 → 9 * * * *
For time-of-day schedules (day at 9am, weekday at 2pm): offset round minutes by a few to avoid API busy marks:
- day at 9am → 3 9 * * *
- day at 14:00 → 3 14 * * *
- weekday at 9am → 3 9 * * 1-5
Deduplicate — use CronList to list existing cron jobs. Use CronDelete to remove any whose prompt starts with Run /fix-issues (prevents duplicate schedules from accumulating).
Reconstruct the arguments for the cron prompt. Always include now in the cron prompt so each cron fire runs immediately AND re-registers itself (self-perpetuating). Note: this now is for the CRON's invocation, not the current invocation — the user controls whether THIS run executes immediately via their own now flag:
```
Run /fix-issues <N> [focus] auto every <schedule> now
```
Create the cron — use CronCreate:
- cron: the cron expression from step 1
- recurring: true
- prompt: the reconstructed command from step 3
Confirm — tell the user, including the estimated wall-clock time of the next run. Compute from the cron expression. Always show times in America/New_York (ET) — use TZ=America/New_York date for conversion, not the system timezone (which may be UTC). Example:

If now is present:

Fix-issues sprint scheduled every 4h. Running now. Next auto-sprint after this one: ~8:15 PM ET (cron ID XXXX).

If now is NOT present:

Fix-issues sprint scheduled every 4h. First run: ~4:15 PM ET (cron ID XXXX). Use /fix-issues next to check, /fix-issues stop to cancel.
If now is present: proceed to Phase 1 (run immediately). If now is NOT present: Exit. The cron will fire at the scheduled time. Do not run a sprint now.

End-of-sprint scheduling note: when a sprint finishes and a cron is active, always include the estimated next run time with timezone in the completion message. Example:

Sprint complete. Next auto-sprint in ~3h 45m (~11:30 PM ET, cron XXXX).

If every is NOT present, skip this phase entirely and proceed to Phase 1 (bare invocation always runs immediately).

Phase 1 — Preflight & Sync

IMPORTANT: Complete ALL steps (1-6 + Phase 1b) before Phase 2. Do NOT skip tracker updates or research to "save time." Dispatching agents without research blurbs causes misinterpretation — agents guess from titles and implement the wrong fix. This has happened repeatedly.

Sprint tracking sentinel

When mode is sprint (N provided), construct the per-sprint unique $SPRINT_ID and $PIPELINE_ID FIRST (before any other tracking write), then create the pipeline sentinel:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
mkdir -p "$MAIN_ROOT/.zskills/tracking"

# Per-sprint unique ID (per Phase 1 design doc OQ3). Prevents concurrent
# fix-issues sessions from colliding on the literal "sprint" suffix. The
# ISSUE_TITLE slug is a human-readable tag; the UTC timestamp guarantees
# uniqueness across concurrent sprints on the same host.
ISSUE_TITLE_SLUG=$(printf '%s' "${ISSUE_TITLE:-sprint}" | tr -cd 'a-z0-9' | head -c 8)
[ -z "$ISSUE_TITLE_SLUG" ] && ISSUE_TITLE_SLUG="sprint"
SPRINT_ID="sprint-$(date -u +%Y%m%d-%H%M%S)-$ISSUE_TITLE_SLUG"
PIPELINE_ID="fix-issues.$SPRINT_ID"
PIPELINE_ID=$(bash scripts/sanitize-pipeline-id.sh "$PIPELINE_ID")
# Recover SPRINT_ID after sanitization (strip the "fix-issues." prefix).
SPRINT_ID="${PIPELINE_ID#fix-issues.}"
mkdir -p "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID"

if [ ! -f "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/pipeline.fix-issues.$SPRINT_ID" ]; then
  printf 'skill: fix-issues\nmode: sprint\ncount: %s\nfocus: %s\nstartedAt: %s\n' \
    "$N" "${FOCUS:-default}" "$(TZ=America/New_York date -Iseconds)" \
    > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/pipeline.fix-issues.$SPRINT_ID"
fi

Preflight checks (before doing anything else)

Before starting the sprint, check for stale state from a previous failed run:

In-progress git operation?
```
ls .git/CHERRY_PICK_HEAD .git/MERGE_HEAD .git/REBASE_HEAD 2>/dev/null
git status --porcelain | grep '^UU\|^AA\|^DD'
```
If either command produces output, the working tree has an unfinished cherry-pick, merge, or rebase — likely from a previous failed sprint. STOP. Invoke the Failure Protocol.

Note: normal uncommitted changes (modified plan files, logs) are expected and are NOT a reason to stop. Phase 6 stashes those before cherry-picking.
Stash stack?
```
git stash list
```
If there is a stash with message containing "pre-cherry-pick", a previous sprint's stash was never restored. STOP. Alert the user — they need to git stash pop or git stash drop before a new sprint can start safely.
Leftover sprint worktrees?
```
git worktree list
```
If worktrees from a previous sprint exist, warn the user. They may contain unapplied fixes. Do not remove them — just note their presence and continue.

If any preflight check fails, invoke the Failure Protocol (kill cron, alert user, write failure to report).

Sync

Fetch all open GitHub issues:

gh issue list --state open --limit 500 --json number,title,labels,createdAt

Run the sync script to find gaps between GitHub and plan files:
```
node ${CLAUDE_SKILL_DIR}/scripts/sync-issues.js
```

Run the stats script to see current distribution:

node ${CLAUDE_SKILL_DIR}/scripts/issue-stats.js

Update ALL issue trackers — scan plans/ for tracker files:
```
ls plans/*ISSUES*.md plans/ISSUES_PLAN.md 2>/dev/null
```
Ensure each tracker reflects current GitHub state. Add new issues to the appropriate tracker based on domain.
Identify gaps — any GH issues not tracked in any plan file? Add them to the appropriate tracker.
Research new issues — for each issue added in step 5 (or any issue lacking a research blurb in its tracker entry), dispatch research agents using the same workflow as the standalone sync command:
1. Read the full issue body (gh issue view <N>)
2. Search the codebase for the affected code
3. Write a concise research blurb (what's wrong, where, suggested approach)
4. Add the blurb to the appropriate tracker file
Without this step, Phase 2 prioritizes from bare titles and Phase 3 dispatches agents with no context — leading to misinterpretation. Past failure: #387 "reset button" was interpreted as "clear canvas" instead of "reset mappings to defaults" because only the title was read.

In auto mode, dispatch research agents in parallel (up to 3 at a time) and proceed after all complete. In interactive mode, present the research blurbs before moving to Phase 1b.

Phase 1b — Read Full Issue Bodies & Plan Context

Before prioritizing, gather full context for every candidate issue:

Fetch the issue body and comments from GitHub:

gh issue view <N> --json number,title,body,labels,comments

Fetch the research blurb from plan files:
```
grep -A 30 '#<N>' plans/*ISSUES*.md 2>/dev/null
```
Plan blurbs contain root cause analysis, affected files, suggested fixes, and effort estimates. This context was gathered when the issue was filed — don't waste time re-researching what's already documented.

Both steps are mandatory. Titles are often vague or misleading. The body and plan blurb together are the spec. You cannot prioritize or write accurate agent prompts without reading both.

For each candidate, note:

What the user actually described (not what the title implies)
Root cause and affected files (from plan blurb)
Repro steps if provided
Suggested fix approach (from plan blurb)
Context metadata (model name, browser, screen size)

Post-preflight tracking

After Phase 1 (preflight + sync + research) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.preflight"

Phase 2 — Prioritize

Present the next N issues to fix as a ranked table:

Priority	#	Title	Severity	Domain	Effort	Tracker

If a focus argument is provided, issues in that domain are boosted to the top, then the remaining slots filled by default priority.

Default ranking criteria (in order):

New issues not yet attempted (user feedback, recently filed)
Correctness defects (from issue trackers tagged as correctness)
Critical/high severity bugs
Quick wins (15 min – 1 hour)
Issues with clear repro steps
Test gaps (from issue trackers tagged as test quality)

Triage: vague, complex, or interrelated issues

While building the ranked list, classify each candidate:

Clear and doable — repro steps, expected behavior, affected files identified. Include in the sprint.
Too vague — no repro steps, no expected behavior, body is empty or just "it's broken." You don't know WHAT to fix.
- Interactive: flag it and ask the user for clarification
- Auto: skip it, report as "Skipped: insufficient context" in SPRINT_REPORT.md
Too complex — clear spec but would require 500+ lines, major refactoring, or architectural changes. Not a batch-fix item.
- Interactive: report "this needs /run-plan, not /fix-issues"
- Auto: skip it, report as "Skipped: too complex for batch fix"
- If plans/PLAN_INDEX.md exists, grep plan files for the issue number (e.g., #NNN). If a plan already covers this issue, note which plan in the skip reason. If no plan covers it, add to the skip note: "Consider /draft-plan for #NNN."

"Too vague" means you don't know WHAT to do — not that you don't know HOW. If the issue clearly describes the problem but the fix is hard, that's not vague — that's work. Never use "vague" as an excuse to skip hard issues.

Group by dependency and file overlap

Before dispatching agents, check for interrelated issues:

Same root cause — if #100 and #101 are both caused by an off-by-one in Solver.js, group them for the same agent. One agent, one worktree, one fix closes both.
Same file — if #200 and #201 both need changes to Parser.js, group them for the same agent. Separate worktrees would produce conflicting cherry-picks.
Prerequisite relationship — if fixing #300 requires the fix from #299 to be in place, give both to the same agent in order.

Tell the agent when issues are related: "Issues #100 and #101 share root cause X in file Y — consider fixing them together with a single commit."

Bundling beyond N. When prioritizing, if additional open issues would naturally be fixed in the same session (same component, same area of code) or appear to have the same root cause, the orchestrator should include them alongside the selected issue for the same agent. These don't count toward N. In interactive mode, show bundled extras in the approval list with the rationale so the user can adjust. This keeps /fix-issues 1 every 1h efficient — one agent, one worktree, but it picks up tightly coupled neighbors instead of leaving them for the next sprint.

Present the list

Without auto: Wait for user approval of the list before proceeding. Include the grouping rationale so the user can adjust.
With auto: Present the ranked table for the record, then proceed immediately using the ranking criteria above.

If no actionable issues found

If ALL candidates are too vague, too complex, or already attempted:

Auto-sync before giving up. Run the full Sync workflow (Steps 1-5). In auto mode, auto-close issues with FIXED verdict (commit hash + tests — the same bar as interactive sync, just without the approval gate). LIKELY FIXED and UNCLEAR still require human judgment and are skipped. Then re-run Phase 1b and Phase 2 to re-evaluate the candidate pool. If actionable issues are now available, proceed to Phase 3 normally.

Only sync once per sprint. If still empty after, proceed to step 2.
If still no actionable issues after refresh:
- Write a minimal sprint section to SPRINT_REPORT.md: ## Sprint — YYYY-MM-DD HH:MM [UNFINALIZED] with "No actionable issues found (synced twice)" and the skip reasons.
- Do NOT kill the cron — new issues may be filed before the next run.
- After 3 consecutive empty runs, add a note: "3 consecutive runs with no actionable issues. Run /fix-issues stop if no new issues are expected." Do NOT auto-stop — that's the user's call.
- Exit. Skip Phases 3-6.

Post-prioritize tracking

After Phase 2 (prioritize) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\nissueCount: %d\n' "$(TZ=America/New_York date -Iseconds)" "$ISSUE_COUNT" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.prioritize"

Phase 3 — Execute (agent teams in worktrees)

In pr mode, the orchestrator creates a NAMED per-issue worktree manually and dispatches agents WITHOUT isolation: "worktree". See the "PR mode (Phase 3)" section below for the exact worktree setup. For cherry-pick and direct modes, use the default isolation: "worktree" pattern described here.

Before dispatching any fix Agent: check agents.min_model in .claude/zskills-config.json. If set, use that model or higher (ordinal: haiku=1 < sonnet=2 < opus=3). Never dispatch with a lower-ordinal model than the configured minimum.

1 issue per agent, parallel dispatch. Each issue gets its own agent in its own worktree (isolation: "worktree" for cherry-pick/direct, or a manually-created fix/issue-NNN worktree for pr mode). Dispatch at most 3 worktree agents per message. If you have more than 3, dispatch the first 3, wait for them to return, then dispatch the next batch. Five concurrent git checkout operations cause I/O contention on 9p filesystems — checkouts stall at ~72% and the Agent framework times out, leaving orphaned worktree directories.

Interrelated issues (same root cause or same files from Phase 2 grouping) share one agent and one worktree. Tell the agent which issues are grouped and why.
Unrelated issues get separate agents. Never batch unrelated hard issues into one agent — this caused a 4.5h bottleneck when one agent got 4 diverse issues sequentially.

Agent timeout: 1 hour. Note the dispatch time for each agent. If an agent hasn't returned after 1 hour, declare it failed:

Mark its issues as "Timed out" in SPRINT_REPORT.md
Issues stay open for the next sprint
The worktree is a cleanup artifact — do NOT auto-land late results
If the agent eventually returns, ignore it. Timed out = failed, period.

Agent dispatch prompts MUST include for each issue:

The verbatim issue body from Phase 1b (gh issue view). Do NOT paraphrase or summarize — include the full text the user wrote. Titles are often vague; the body is the spec. If the body is empty, say so explicitly.
The research blurb from issue tracker files (plans/*ISSUES*.md). These contain root cause analysis, affected files, suggested fixes, and effort estimates written when the issue was filed. Grep the tracker files for the issue number and include any matching section verbatim.

The agent should have everything it needs to understand the problem without re-researching from scratch. Missing context = wrong fix.

For issue bodies or plan blurbs longer than ~100 lines: write the verbatim text to a temp file (e.g., /tmp/issue-NNN.md) and tell the agent to Read the file. This avoids the natural LLM tendency to compress long text when inlining it in a prompt. Shorter content can be inlined directly.

Declare pipeline ID early in execution (before any git operation). $PIPELINE_ID was constructed at the top of Phase 1 ("Sprint tracking sentinel") as fix-issues.$SPRINT_ID:

echo "ZSKILLS_PIPELINE_ID=$PIPELINE_ID"

Before dispatching each fix agent to its worktree, write .zskills-tracked:

printf '%s\n' "$PIPELINE_ID" > "<worktree-path>/.zskills-tracked"

The echo associates the orchestrator session with this pipeline (read by hook from transcript). The .zskills-tracked file associates each worktree agent.

Each agent follows this fix workflow:

Read the issue body (included in prompt) and relevant code
Reproduce the bug (unit test or manual)
Implement the fix
Write regression tests (unit and/or E2E as appropriate)
Run npm run test:all — all suites must pass
Agent verification via /manual-testing if UI files changed — use playwright-cli with real events, take screenshots as evidence. The pre-commit hook will BLOCK your commit if UI files are staged but playwright-cli wasn't used in the session. This is not optional.
Classify User Verify — if any UI/editor/styles files changed (check your project's UI directories), mark User Verify: NEEDED in the sprint report. The user must see UI changes before the issue can be closed. This is in ADDITION to your agent verification.
Commit in the worktree (one issue per commit, clean history)
Rebase onto current main before final commit:
```
git fetch origin main && git rebase origin/main
```
This ensures the commit contains only the agent's changes, not stale copies of files other agents already fixed on main. If rebase conflicts, abort (git rebase --abort) and proceed — Phase 6 cherry-pick verification will catch stale files via selective extraction.

The implementation agent does NOT commit. The verification agent runs the full test suite and commits if verification passes. This ensures the hook's test gate is satisfied. The approval gate is landing to main (Phase 6).

PR mode (Phase 3)

When LANDING_MODE == pr, each issue gets its own named branch and worktree (one PR per issue, unlike /run-plan PR mode where all phases share one branch).

Differences from /run-plan PR mode:

Branch prefix is hardcoded fix/ (not config branch_prefix)
Branch name uses the issue number, not a plan slug
Worktree path uses fix-issue-NNN, not pr-<plan-slug>
One worktree per issue (not one per plan)

Branch naming: fix/issue-NNN where NNN is the GitHub issue number.

Worktree path: /tmp/<project-name>-fix-issue-NNN

ISSUE_NUM=42
BRANCH_NAME="fix/issue-${ISSUE_NUM}"
PROJECT_NAME=$(basename "$PROJECT_ROOT")
WORKTREE_PATH="/tmp/${PROJECT_NAME}-fix-issue-${ISSUE_NUM}"

# Prune stale worktree entries. If /tmp was cleared (container restart,
# codespace rebuild), git still has the old worktree registered in
# .git/worktrees/. `git worktree prune` cleans up entries whose directories
# no longer exist, so `git worktree add` won't fail with "already registered."
git worktree prune

# Orchestrator creates worktree manually -- NOT via isolation: "worktree"
if [ -d "$WORKTREE_PATH" ]; then
  echo "Resuming existing fix worktree at $WORKTREE_PATH"
else
  # Legitimate multi-phase PR-mode resume — opt into branch resume.
  ZSKILLS_ALLOW_BRANCH_RESUME=1 \
    bash scripts/worktree-add-safe.sh "$BRANCH_NAME" "$WORKTREE_PATH" main
fi

# Pipeline association -- agent commits are gated by .zskills-tracked
echo "$PIPELINE_ID" > "$WORKTREE_PATH/.zskills-tracked"

Dispatching fix agents in PR mode: Dispatch agents WITHOUT isolation: "worktree" — the worktree already exists. The agent prompt must include FIRST: cd $WORKTREE_PATH as the mandatory first action. Without this instruction, the agent starts in the main repo.

For grouped interrelated issues (same root cause or same files from Phase 2 grouping), pick the LOWEST issue number as the branch identifier (fix/issue-NNN) and include all grouped issues in that one worktree. The .landed marker's issue: field records the primary issue; group members are listed separately in the sprint report.

Post-execute tracking

After Phase 3 (execute) is complete — all agents have returned:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.execute"

Phase 4 — Review

Pre-verification tracking

Before dispatching verification agents, create a delegation requirement marker so the hook can enforce that verification actually runs. The marker lives in fix-issues' own per-sprint subdir (same pattern as run-plan's delegation lock in Phase 3 of the tracking plan):

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
mkdir -p "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID"
printf 'skill: verify-changes\nparent: fix-issues\nmode: sprint\ndate: %s\n' \
  "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/requires.verify-changes.$SPRINT_ID"

Dispatch protocol

Check your tool list. If Agent (or Task) is in your tool list, you are at top level — dispatch fresh verification subagents per the protocol below. The implementation subagents (in their per-issue worktrees) and the verification subagent are sibling subagents of you, the top-level orchestrator. The verifier has no memory of what the implementer did because they're separate contexts.

If you do NOT have the Agent tool, you are running as a subagent yourself (Claude Code subagents have no Agent tool, by Anthropic's design at https://code.claude.com/docs/en/sub-agents). Run /verify-changes worktree inline in your current context, once per worktree. This is single-context inline verification — flag in the report whether you were fresh relative to the implementer or not. This fallback is mostly defensive since /fix-issues typically runs at top level.

Before dispatching any verification Agent: check agents.min_model in .claude/zskills-config.json. If set, use that model or higher (ordinal: haiku=1 < sonnet=2 < opus=3). Never dispatch with a lower-ordinal model than the configured minimum.

After each agent completes, dispatch a fresh agent to run /verify-changes worktree in its worktree. Do NOT run verification yourself — you wrote the dispatch prompts, so you have implementer bias. The verification agent must be a fresh agent with no memory of the implementation.

This delegates the full review workflow (diff review, test coverage audit, test run, manual verification, fix & re-verify cycle) to a separate agent.

Report the review results to the user.

Post-verify tracking

After Phase 4 (verify) is complete — all verification agents have returned:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.verify"

Phase 5 — Write Sprint Report (BEFORE landing)

APPEND a new sprint section to SPRINT_REPORT.md BEFORE Phase 6 (landing). The report is a prerequisite for landing — if it's not written, Phase 6 does not execute.

APPEND, do not overwrite. Multiple sprints may run between /fix-report reviews (e.g., cron every 2h, user checks once a day). Each sprint adds a new ## Sprint — YYYY-MM-DD HH:MM [UNFINALIZED] section. /fix-report processes all UNFINALIZED sections when the user reviews.

If the file doesn't exist, create it with a # Sprint Report heading.

Past failure: an agent skipped Phase 5 for 8 consecutive sprints to "keep the hourly cadence fast." SPRINT_REPORT.md was stale for 8 sprints, making /fix-report useless. Another failure: the file was overwritten each sprint, losing results from earlier sprints that were never reviewed.

Report format — each sprint appends a section like this:

## Sprint — YYYY-MM-DD HH:MM [UNFINALIZED]

**Mode:** auto | interactive | **Focus:** <focus> | default

### Fixed
| # | Title | Worktree | Commit | Tests | Agent Verify | User Verify |
|---|-------|----------|--------|-------|-------------|-------------|
| #123 | Solver crash | wt-123 | abc1234 | 2 unit | PASS (tests) | N/A |
| #456 | Button offset | wt-456 | def5678 | 1 E2E | PASS (screenshot) | NEEDED |

**Agent Verify:** Did the agent test it? PASS (with method) or SKIPPED.
The pre-commit hook blocks commits without test evidence.

**User Verify:** Does the user need to see this? Mechanically classified:
if any UI/editor/styles files changed → `NEEDED`. Otherwise → `N/A`.
`/fix-report` Step 2
presents all `NEEDED` items for user review before closing.

### Skipped — Too Vague (need repro steps or clearer spec)
| # | Title | What's Missing |
|---|-------|----------------|

### Skipped — Too Complex (need /run-plan)
| # | Title | Why |
|---|-------|-----|

### Skipped — Cherry-Pick Conflict (will retry next sprint)
| # | Title | Conflict Details |
|---|-------|-----------------|
| #789 | Parser error | cherry-pick conflict on commit abc1234 |

### Not Fixed (agent attempted but failed)
| # | Title | Reason |
|---|-------|--------|

The file starts with # Sprint Report (created once). Each sprint appends a new ## Sprint section. /fix-report marks sections [FINALIZED] after review. Use actual data — real issue numbers, commit hashes, worktree paths, and test counts.

Post-report tracking

After Phase 5 (report) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.report"

Phase 6 — Land

Landing mode dispatch:

LANDING_MODE == cherry-pick — default path (below).
LANDING_MODE == pr — see "PR mode landing" subsection. One PR per fixed issue, with Fixes #NNN linking.
LANDING_MODE == direct — no-op: work was committed on main by the verification agent (no worktree isolation was used). Proceed to post-land tracking. Note: direct mode still requires the verification agent to commit — it just doesn't cherry-pick or push to a branch.
Without auto: Sprint complete. Output:

Sprint complete. Report written to SPRINT_REPORT.md. Run /fix-report to review fixes, land to main, and close issues.

All interactive landing, closing, and cleanup moves to /fix-report. /fix-issues is DONE after writing the report.
With auto: Auto-land verified fixes to main:
1. Try cherry-picking WITHOUT stashing first. Git allows cherry-picks on a dirty working tree as long as the cherry-picked files don't overlap with uncommitted changes. Other sessions may have uncommitted work in the tree — stashing captures THEIR changes too, and the pop can silently merge or lose them. Past failure: stash/pop cycle during cherry-pick wiped out another session's skill changes.
  
  If git refuses with "your local changes would be overwritten," the cherry-pick touches files with uncommitted changes. Handle with LLM-assisted merge:
  1. Note which files overlap
  2. Capture the pre-stash state of each overlapping file: git diff <file> — save/remember this output. It's your evidence of what the uncommitted changes were (possibly from another session).
  3. git stash -u -m "pre-cherry-pick stash"
  4. git cherry-pick <commit-hash>
  5. git stash apply (NOT pop — keep the stash as a recovery path)
  6. If stash apply produces conflict markers (<<<<<<<), resolve them — read both sides and combine. This is expected for overlaps.
  7. For every overlapping file, READ the result and compare against the pre-stash diff from step 2. Verify every changed line from the uncommitted changes is still present AND the cherry-pick's fix landed correctly. If the merge dropped changes, restore them.
  8. After verification, drop the stash: git stash drop
  9. If you genuinely can't reconcile (same lines, conflicting purposes), STOP and report to the user.
2. Verify main is clean before cherry-picking:
```
npm run test:all
```
  If main's tests are already failing, STOP. Invoke the Failure Protocol — do not cherry-pick on top of broken code. Report: "main is broken before cherry-pick. Fix main first."
3. Cherry-pick sequentially — one commit at a time, verify each succeeds before the next. Try without stash first (step 1). Only stash if git refuses due to file overlap.
4. If a cherry-pick conflicts: abort and skip that worktree's commits. If the worktree has multiple commits (grouped interrelated issues), skip ALL of them — they likely depend on each other.
```
git cherry-pick --abort
```
  Mark the issues as "Skipped: cherry-pick conflict" in SPRINT_REPORT.md. Continue cherry-picking from other worktrees. Do NOT invoke the Failure Protocol for skipped worktrees.
  
  The skipped issues stay open and will be picked up in the next sprint — by then the conflicting fix is on main, so the conflict resolves itself.
5. Extract logs and mark worktrees as landed — for each worktree whose commits were successfully cherry-picked: a. Copy unique session logs to main:
```
if [ -d "<worktree>/.claude/logs" ]; then
  for log in <worktree>/.claude/logs/*.md; do
    [ -f ".claude/logs/$(basename $log)" ] || cp "$log" .claude/logs/
  done
fi
```
  b. Write .landed marker (atomic):
```
cat <<LANDED | bash scripts/write-landed.sh "<worktree>"
status: full
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
commits:
  <list of cherry-picked commit hashes and messages>
LANDED
```
  c. For tiers that were SKIPPED (conflict), write partial marker:
```
cat <<LANDED | bash scripts/write-landed.sh "<worktree>"
status: partial
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
landed: <hashes that did land, if any>
skipped: <hashes that conflicted>
reason: cherry-pick conflict
LANDED
```
6. Commit extracted logs:
```
git add .claude/logs/
git commit -m "chore: session logs from fix-issues sprint"
```
7. Restore stash if one was created:
```
git stash pop
```
8. Run tests after all cherry-picks land:
```
npm run test:all
```
  If tests fail, invoke the Failure Protocol — do not leave broken code on main with the cron still running.
9. Update SPRINT_REPORT.md — mark which fixes were landed (add a Landed column or update status).
10. Auto-remove fully landed worktrees — for each worktree with status: full in .landed:
```
# Logs already extracted in step 5a. Double-check for stragglers:
if [ -d "<worktree>/.claude/logs" ]; then
  for log in <worktree>/.claude/logs/*.md; do
    [ -f ".claude/logs/$(basename "$log")" ] || cp "$log" .claude/logs/
  done
fi

# Check for real uncommitted work (not artifacts)
DIRTY=$(git -C "<worktree>" diff --name-only HEAD)
UNTRACKED=$(git -C "<worktree>" status --porcelain | \
  grep -v '\.landed\|\.worktreepurpose\|\.test-results\|\.playwright\|node_modules')

if [ -z "$DIRTY" ] && [ -z "$UNTRACKED" ]; then
  rm -f "<worktree>/.landed" "<worktree>/.worktreepurpose"
  git worktree remove "<worktree>"
  git branch -d "<branch>" 2>/dev/null
else
  echo "Worktree <name> not auto-removed: uncommitted work found"
fi
```
  Skip removal for worktrees with status: partial — those have unapplied commits that need attention.
11. Done. Closing GH issues and updating trackers are still /fix-report actions — even in auto mode.

PR mode landing

When LANDING_MODE == pr, landing replaces cherry-pick with per-issue rebase + push + PR creation + CI + auto-merge. Each fixed issue is handled independently: one branch, one PR, one .landed marker per worktree. A failure on one issue (rebase conflict, CI failure, PR creation error) does NOT block the others — mark that issue's status and continue to the next.

Loop over every fixed issue (and any grouped issue worktrees from Phase 2). $FIXED_ISSUES is the list of issue numbers whose worktrees have verified commits on fix/issue-NNN.

Rebase before push (same pattern as /run-plan PR mode rebase point 2, but per issue — fix-issues is single-phase per issue, so only one rebase point is needed):

cd "$WORKTREE_PATH"
git fetch origin main
PRE_REBASE=$(git rev-parse HEAD)
git rebase origin/main
if [ $? -ne 0 ]; then
  # Abort and mark this issue as conflict. Continue to the next issue.
  if [ -d "$(git rev-parse --git-dir)/rebase-merge" ] || \
     [ -d "$(git rev-parse --git-dir)/rebase-apply" ]; then
    git rebase --abort
  fi
  echo "REBASE CONFLICT for issue #$ISSUE_NUM."
  cat <<LANDED | bash scripts/write-landed.sh "$WORKTREE_PATH"
status: conflict
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
method: pr
branch: $BRANCH_NAME
issue: $ISSUE_NUM
reason: rebase-conflict
LANDED
  continue  # Move to next issue
fi
if [ "$(git rev-parse HEAD)" != "$PRE_REBASE" ]; then
  echo "Main moved -- re-verifying issue #$ISSUE_NUM before push..."
  # Dispatch /verify-changes worktree re-verification.
  # Agent prompt includes "FIRST: cd $WORKTREE_PATH".
  # Re-verification has its own fix cycle (max 2 attempts), independent
  # of the CI fix budget. If re-verification fails after its own max
  # attempts, mark the issue as pr-failed and move on.
fi

Push + PR creation (per issue):

for issue in "${FIXED_ISSUES[@]}"; do
  ISSUE_NUM="$issue"
  BRANCH_NAME="fix/issue-${ISSUE_NUM}"
  PROJECT_NAME=$(basename "$PROJECT_ROOT")
  WORKTREE_PATH="/tmp/${PROJECT_NAME}-fix-issue-${ISSUE_NUM}"

  # Fetch issue title for the PR title
  ISSUE_TITLE=$(gh issue view "$ISSUE_NUM" --json title --jq '.title' 2>/dev/null || echo "Issue $ISSUE_NUM")

  cd "$WORKTREE_PATH"

  # Push (new or update)
  if git ls-remote --heads origin "$BRANCH_NAME" | grep -q "$BRANCH_NAME"; then
    echo "Remote branch $BRANCH_NAME already exists. Pushing updates."
    git push origin "$BRANCH_NAME"
  else
    git push -u origin "$BRANCH_NAME"
  fi

  # Existing PR? Update, don't duplicate.
  EXISTING_PR=$(gh pr list --head "$BRANCH_NAME" --json number --jq '.[0].number' 2>/dev/null)
  if [ -n "$EXISTING_PR" ]; then
    PR_URL=$(gh pr view "$EXISTING_PR" --json url --jq '.url')
    PR_NUMBER="$EXISTING_PR"
  else
    PR_URL=$(gh pr create \
      --title "Fix #${ISSUE_NUM}: ${ISSUE_TITLE}" \
      --body "$(cat <<EOF
Fixes #${ISSUE_NUM}

## Changes
${CHANGE_SUMMARY}

## Test plan
- [ ] Verify the fix resolves the original issue
- [ ] All existing tests pass
EOF
)" \
      --base main \
      --head "$BRANCH_NAME")
    if [ -n "$PR_URL" ]; then
      PR_NUMBER=$(gh pr view --json number --jq '.number')
    fi
  fi

  # If PR creation failed, write pr-failed marker and continue.
  if [ -z "$PR_URL" ]; then
    echo "WARNING: PR creation failed for issue #$ISSUE_NUM. Branch pushed but PR not created."
    cat <<LANDED | bash scripts/write-landed.sh "$WORKTREE_PATH"
status: pr-failed
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
method: pr
branch: $BRANCH_NAME
issue: $ISSUE_NUM
pr:
commits: $(git log main.."$BRANCH_NAME" --format='%h' | tr '\n' ' ')
LANDED
    continue
  fi

  # --- CI check + auto-merge: same pattern as /run-plan 3b-iii ---
  # See skills/run-plan/SKILL.md "PR mode landing" for the canonical
  # implementation: config re-read, pre-check retry, polling, fix cycle,
  # auto-merge, .landed upgrade.
  #
  # Differences from /run-plan PR mode:
  #   - source: "fix-issues" (not "run-plan")
  #   - .landed marker includes `issue: $ISSUE_NUM`
  #   - `timeout 300` per issue (NOT 600) to avoid serial accumulation
  #     across N issues. If CI doesn't resolve in 5 min for a given issue,
  #     write status: pr-ready and move on. The next cron turn or the
  #     user re-checks.
  #
  # Parallel optimization (future): if the orchestrator can dispatch
  # sub-agents, each issue's CI polling can run in parallel. Not required
  # for initial implementation.

  # --- .landed marker (per issue) ---
  # $LANDED_STATUS, $CI_STATUS, $PR_STATE come from the CI/auto-merge block.
  cat <<LANDED | bash scripts/write-landed.sh "$WORKTREE_PATH"
status: $LANDED_STATUS
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
method: pr
branch: $BRANCH_NAME
pr: $PR_URL
ci: $CI_STATUS
pr_state: $PR_STATE
issue: $ISSUE_NUM
commits: $(git log main.."$BRANCH_NAME" --format='%h' | tr '\n' ' ')
LANDED

  echo "Issue #$ISSUE_NUM -> PR: $PR_URL (status: $LANDED_STATUS)"

  # Cleanup on merge: same as /run-plan PR mode -- if status is `landed`
  # (PR merged), call land-phase.sh to remove the worktree.
  if [ "$LANDED_STATUS" = "landed" ]; then
    bash scripts/land-phase.sh "$WORKTREE_PATH"
  fi
done

.landed status values for PR mode (same as /run-plan):

Scenario	status	method	ci	pr_state
PR merged (auto-merge)	`landed`	`pr`	`pass`/`none`/`skipped`	`MERGED`
PR open, CI passed, awaiting review	`pr-ready`	`pr`	`pass`/`none`/`skipped`	`OPEN`
PR open, CI timed out (still running)	`pr-ready`	`pr`	`pending`	`OPEN`
PR open, CI failing after max attempts	`pr-ci-failing`	`pr`	`fail`	`OPEN`
Branch pushed, PR creation failed	`pr-failed`	`pr`	(not set)	(not set)
Rebase conflict	`conflict`	`pr`	(not set)	(not set)

In all PR mode markers, the issue: field records which GitHub issue the branch resolves. /fix-report reads this field to group PR URLs with issue numbers in the sprint summary.

Post-land tracking

After Phase 6 (land) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.land"

After the sprint completes (whether all issues landed or the sprint ended), clean up the sentinel:

rm -f "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/pipeline.fix-issues.$SPRINT_ID"

Also remove .zskills-tracked from each worktree that was used.

Failure Protocol

If anything goes wrong during an auto or every sprint — cherry-pick conflict, test failures after landing, agent crash, API errors that block progress — execute these steps in this exact order:

1. Kill the cron FIRST

This is the most critical step. A broken sprint leaves state that a subsequent cron run will stomp on — partially landed cherry-picks, active stashes, conflicted working trees, dangling worktrees. The next run doesn't know about any of this and will blindly stash, cherry-pick, and overwrite.

CronList → find the /fix-issues job ID → CronDelete

Do this BEFORE any cleanup or reporting. Even if you're about to fix the problem, kill the cron. The user can restart it after reviewing.

2. Restore the working tree

If a cherry-pick is in a conflicted state:

git cherry-pick --abort

If a stash was created during Phase 6 auto-land:

git stash pop

If git stash pop conflicts, do NOT attempt to clean up. Do NOT git stash drop (destroys untracked files). Do NOT git checkout -- . (also destroys untracked files extracted during the failed pop). The conflicted state preserves all data — leave it as-is and report to the user:

Stash pop conflicts. Stash preserved (contains untracked files). Run git stash show to inspect, then git stash pop manually.

Never destroy work to clean up. It's always better to STOP with a messy state than to lose files trying to clean up.

3. Write the failure to SPRINT_REPORT.md

Create the file if it doesn't exist (preflight failures happen before Phase 5 creates it). If it already exists, add the failure section immediately after the # Sprint Report heading.

Add a ## Sprint Failed section at the top of the report:

## Sprint Failed — YYYY-MM-DD HH:MM

**Phase:** [which phase failed]
**Error:** [what went wrong]
**State:**
- Cherry-picks landed before failure: [list or "none"]
- Stash restored: yes/no
- Worktrees with changes: [list]
- Cron killed: yes (was job ID XXXX)

**To resume:** Review the state above, then either:
- Run `/fix-report` to finalize what succeeded
- Run `/fix-issues ... every` to restart the cron after resolving

4. Alert the user

Output a clear, prominent message:

⚠ SPRINT FAILED — cron stopped

Phase N failed: [one-line reason]
[specific error details]

What happened:
  - [N] fixes were in worktrees, [M] were cherry-picked to main before failure
  - Stash was [restored / not needed]
  - Cron job [ID] has been CANCELLED — no more auto-runs until you restart

Working tree is clean. See SPRINT_REPORT.md for full details.
To restart: /fix-issues N auto every SCHEDULE now
To cancel: /fix-issues stop

Do not bury the failure in normal output. The user needs to see immediately that something broke, the cron is stopped, and what state was left behind.

When to trigger

Invoke this protocol for ANY of these:

npm run test:all fails after cherry-picks are landed (Phase 6 step 8) Note: cherry-pick CONFLICTS are handled by skip-and-continue (Phase 6 step 4), NOT the Failure Protocol. The protocol is only for test failures and unrecoverable errors.
The sprint globally produces 0 fixes (every agent failed or returned no commits) — note: this means ALL agents, not a single agent failing
GitHub API errors that prevent issue fetching
Preflight checks detect stale state (conflict markers, orphaned stash)
Any unrecoverable error that stops the sprint from completing normally

Do NOT invoke for:

Individual agent test failures in worktrees (those are reported in the sprint report as "Not Fixed" — the sprint continues with remaining fixes)
Warnings or non-blocking issues
Pre-existing test failures unrelated to the sprint

For failed/abandoned worktrees: when an agent returns no commits, crashes, or times out, the ORCHESTRATOR (not the failed agent) writes a failure marker on the worktree:

cat <<LANDED | bash scripts/write-landed.sh "<worktree>"
status: failed
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
issues: <issue numbers attempted>
reason: <agent returned no commits / agent crashed / tests failed>
LANDED

This ensures /fix-report can distinguish failed worktrees from active ones. The issues stay open for the next sprint.

Key Rules

Worktrees only — all fixes happen in isolated worktrees, never in the main working tree.
The verification agent commits after passing tests — the implementation agent does not commit. This satisfies the hook's test gate.
Never cherry-pick to main without permission — unless auto flag is set, in which case the user has pre-approved autonomous landing.
In auto mode, skip conflicting cherry-picks — abort the conflict, skip all commits from that worktree (grouped issues depend on each other), mark as "Skipped: conflict" in the report, and continue landing from other worktrees. The skipped issues self-heal next sprint.
Always write SPRINT_REPORT.md — it's the handoff to /fix-report.
Never close GH issues, update trackers, or remove worktrees — that's /fix-report's job.
One issue per commit — clean git history in worktrees.
npm run test:all before every commit — not just npm test.
Never weaken tests — fix the code, not the test. Do not loosen tolerances, skip assertions, or remove test cases.
Never defer the hard parts — finish all phases of the plan. Do not stop after the easy part and call remaining work "future phases."
Protect untracked files — before stash/cherry-pick/merge, inventory untracked files (git status -s | grep '^??'). Use git stash -u or save them first.
every implies auto — scheduling only makes sense for autonomous runs. If every is present but auto is not, treat it as if auto was set.
Deduplicate crons — always remove existing /fix-issues crons before creating a new one. Never let duplicate schedules accumulate.
Crons are session-scoped — they expire when the session dies. Tell the user to re-run /fix-issues ... every to restart scheduling.
Kill the cron on failure — if anything in the sprint fails unrecoverably, the FIRST action is CronDelete. A broken sprint + live cron = the next run stomps on the bad state. See the Failure Protocol for the full sequence.
Read every issue body before acting — gh issue view <N> is mandatory in Phase 1b. Titles are often vague or misleading. The body is the spec. Never paraphrase — include verbatim issue text in agent dispatch prompts. Past failure: #387 title "reset button" was interpreted as "clear canvas" instead of "reset mappings to defaults" because only the title was read.
Ultrathink — use careful, thorough reasoning. Read code, understand what changed and why, verify correctness.

name	fix-issues
disable-model-invocation	true
argument-hint	N [focus] [auto] [every SCHEDULE] [now] \| sync \| plan [auto] \| stop \| next
description	Orchestrate a batch bug-fixing sprint. Supports scheduling with every/now/next/stop. Use sync to update trackers and verify/close already-fixed issues. Use plan to draft plans for skipped issues. Usage: /fix-issues N [focus] [auto] [every SCHEDULE] [now] \| sync \| plan [auto] \| stop \| next.

/fix-issues N [focus] [auto] [every SCHEDULE] [now] | sync | plan [auto] | stop | next — Batch Bug-Fixing Sprint

Ultrathink throughout. Use careful, thorough reasoning at every step.

Arguments

/fix-issues N [focus] [auto] [every SCHEDULE] [now]
/fix-issues sync | plan [auto] | stop | next

N (required for sprints) — number of issues to fix (e.g., 30)
focus (optional) — prioritize a specific domain. The agent scans plans/*_ISSUES.md and plans/ISSUES_PLAN.md to discover tracker files and their domains. Common focus values: new, correctness, codegen, ui, tests — but any domain found in your tracker files works. Omit for default priority order.
auto (optional) — bypass confirmation gates for autonomous operation. Behavior depends on context:
- Sprints: skip Phase 2 issue list approval, auto-land to main via cherry-pick. Does NOT close GH issues or remove worktrees — those are /fix-report actions.
- plan auto: draft plans for all found issues without selection (see Plan section).
- Not applicable to sync. sync is always interactive — closing issues on GitHub requires human approval.
every SCHEDULE (optional) — self-schedule recurring runs via cron:
- Accepts intervals: 4h, 2h, 30m, 12h
- Accepts time-of-day: day at 9am, day at 14:00, weekday at 9am
- Without now: schedules only, does NOT run immediately
- With now: schedules AND runs immediately
- Implies auto — scheduling only makes sense for autonomous runs
- Each run re-registers the cron (self-perpetuating)
- Cron is session-scoped — dies when the session dies
now (optional) — run immediately. When combined with every, runs immediately AND schedules. Without every, now is the default behavior (bare invocation always runs immediately).
sync — update all issue tracker files from GitHub, research new issues, AND verify/close issues that appear already fixed. Dispatches research agents that also check if open issues are already resolved in the codebase. Always interactive — presents findings and asks before closing. See Sync section for the full flow.
plan — draft plans for issues previously skipped as "too complex." Scans SPRINT_REPORT.md for skipped items, dispatches /draft-plan for each. No fixing — just creates plans for /run-plan to execute later.
stop — cancel any existing /fix-issues cron and exit. Takes precedence over all other arguments.
next — check when the next scheduled run will fire. Takes precedence over all other arguments except stop.
pr (optional) — land each fixed issue via a per-issue PR on a named branch (fix/issue-NNN) in a dedicated worktree. Overrides the config default execution.landing.
direct (optional) — land each fixed issue directly on main (no worktree isolation, no PR). Overrides the config default. Incompatible with execution.main_protected: true.

Detection: scan $ARGUMENTS for:

stop (case-insensitive) — cancel cron and exit (highest precedence)
next (case-insensitive) — check schedule and exit
sync (case-insensitive) — sync trackers, verify/close fixed issues, and exit
plan (case-insensitive) — draft plans for skipped issues and exit
now (case-insensitive) — run immediately
auto (case-insensitive) — autonomous mode (behavior varies by context)
every followed by a schedule expression — scheduling mode
pr (case-insensitive) — PR landing mode (per-issue branches + PRs)
direct (case-insensitive) — direct landing mode (commit on main)

Landing mode resolution (same pattern as /run-plan):

Explicit argument wins: pr or direct in $ARGUMENTS
Config default: read .claude/zskills-config.json execution.landing field
Fallback: cherry-pick

# Detect landing mode (same logic as /run-plan)
LANDING_MODE="cherry-pick"
if [[ "$ARGUMENTS" =~ (^|[[:space:]])[pP][rR]($|[[:space:]]) ]]; then
  LANDING_MODE="pr"
elif [[ "$ARGUMENTS" =~ (^|[[:space:]])[dD][iI][rR][eE][cC][tT]($|[[:space:]]) ]]; then
  LANDING_MODE="direct"
else
  CONFIG_FILE="$PROJECT_ROOT/.claude/zskills-config.json"
  if [ -f "$CONFIG_FILE" ]; then
    CONFIG_CONTENT=$(cat "$CONFIG_FILE")
    if [[ "$CONFIG_CONTENT" =~ \"landing\"[[:space:]]*:[[:space:]]*\"([^\"]*)\" ]]; then
      CFG_LANDING="${BASH_REMATCH[1]}"
      [ -n "$CFG_LANDING" ] && LANDING_MODE="$CFG_LANDING"
    fi
  fi
fi

# Validation: direct + main_protected -> error
if [[ "$LANDING_MODE" == "direct" ]]; then
  CONFIG_FILE="$PROJECT_ROOT/.claude/zskills-config.json"
  if [ -f "$CONFIG_FILE" ]; then
    CONFIG_CONTENT=$(cat "$CONFIG_FILE")
    if [[ "$CONFIG_CONTENT" =~ \"main_protected\"[[:space:]]*:[[:space:]]*true ]]; then
      echo "ERROR: direct mode is incompatible with main_protected: true. Use pr mode or change config."
      exit 1
    fi
  fi
fi

Examples:

/fix-issues 30 — interactive, 30 issues, run now
/fix-issues 10 correctness — interactive, solver focus, run now
/fix-issues 5 auto — autonomous, one-time, run now
/fix-issues 5 auto every 4h — schedule every 4h (first run in ~4h)
/fix-issues 5 auto every 4h now — schedule every 4h + run immediately
/fix-issues 10 auto every day at 9am — schedule daily at 9am
/fix-issues 10 auto every weekday at 9am now — schedule + run now
/fix-issues sync — update trackers + verify/close fixed issues (always interactive)
/fix-issues plan — draft plans for issues skipped as "too complex"
/fix-issues plan auto — same, but plan all without selection
/fix-issues stop — cancel the recurring cron
/fix-issues next — check when the next sprint will run
/fix-issues 5 auto pr — autonomous sprint, per-issue PR landing
/fix-issues 3 auto direct — autonomous sprint, land commits on main directly

Now (standalone — no N provided)

If $ARGUMENTS is just now (no N, no focus, no every — just the word now by itself):

Use CronList to list all cron jobs
Find any whose prompt starts with Run /fix-issues
If found: extract the cron's prompt to get N, focus, auto, and schedule. Run the sprint immediately using those parameters — proceed to Phase 1 with the cron's N, focus, and auto settings. Do NOT ask for confirmation — now IS the confirmation. The cron itself stays active.
If none found: report No active /fix-issues cron to trigger. Use /fix-issues N to run manually. and exit.

Next (if `next` is present)

If $ARGUMENTS contains next (case-insensitive):

Use CronList to list all cron jobs
Find any whose prompt starts with Run /fix-issues
Report:
- If found: parse the cron expression and compute the next fire time. Use date +%Z for the timezone. Show both relative and absolute:
  
  Next fix-issues sprint in ~2h 15m (~8:30 PM ET, cron XXXX). Prompt: Run /fix-issues 5 auto every 4h
- If none found: No active /fix-issues cron in this session.
Exit. Do not proceed to any phase.

Stop (if `stop` is present)

If $ARGUMENTS contains stop (case-insensitive):

Use CronList to list all cron jobs
Delete ALL whose prompt starts with Run /fix-issues using CronDelete
Report what was cancelled:
- If one cron found: Fix-issues cron stopped (was job ID XXXX, every INTERVAL).
- If multiple found: Stopped N fix-issues crons (IDs: XXXX, YYYY).
- If none found: No active /fix-issues cron found.
Exit. Do not proceed to any phase. The stop command does nothing else.

Sync (if `sync` is present)

Step 1 — Fetch & update trackers

Run Phase 1a (Preflight & Sync) — fetch all open issues, run sync script, update all tracker files.

Step 2 — Research & verify

Dispatch research agents for every open issue that lacks a research blurb in its tracker file. Each agent does:

Read the full issue body and comments from GitHub
Grep the codebase for related files and code
Write a concise research blurb (what's wrong, where, suggested approach)
Add the blurb to the appropriate tracker file

FIXED — code fix is present AND tests pass. Include: commit hash, what changed, which tests cover it.
LIKELY FIXED — code fix appears present but no specific tests cover this exact issue. Include what was found and what's missing.
NOT FIXED — the reported problem still exists in the code (normal — this is just a research blurb, the issue stays open).
UNCLEAR — can't determine from code review alone (needs manual testing).

Criteria for FIXED/LIKELY FIXED verdicts:

The specific code the issue reported as broken has been changed
Tests exist that cover the reported behavior (FIXED) or not (LIKELY FIXED)
The fix commit references the issue number or is clearly related
Do NOT verdict as FIXED if: the issue is a feature request (not a bug), the fix is partial, or you're not confident

Also scan for additional close candidates from:

Tracker files — [x] items that are still open on GitHub
Sprint reports — entries in "Already Implemented" or "Already Fixed on Main" sections of SPRINT_REPORT.md

For these candidates, dispatch verification agents with the same checklist above (read issue body, check code, check tests, produce verdict).

Step 3 — Present findings

Show the sync summary and any close candidates:

Sync complete. N open issues, M newly researched, K tracker files updated.
Gaps: [any GH issues not in any tracker]

Issues that appear already fixed (N candidates):

| # | Title | Verdict | Evidence |
|---|-------|---------|----------|
| #126 | Fcn block mapping | FIXED | SlxImporter.js:85, commit abc1234, 2 tests |
| #191 | Block stubs | FIXED | All 4 blocks implemented, 12 tests pass |
| #393 | Fcn codegen u(N) | FIXED | codegen emitter step 8, commit def5678 |
| #200 | Some bug | LIKELY FIXED | Code changed but no regression test |

Close 3 FIXED issues? (all / comma-separated numbers / none)

Wait for user selection. LIKELY FIXED and UNCLEAR items are shown for context but NOT offered for closing — they need human judgment.
If no close candidates found: skip this step, just show the sync summary.

Step 4 — Close approved issues on GitHub

For each approved issue:

Close with a comment explaining what fixed it:

gh issue close <N> --comment "Fixed in commit <hash>. <brief description of fix>. Tests: <test file(s)>."

Update tracker files — mark the issue [x] in all relevant trackers.
Update SPRINT_REPORT.md — if the issue appears in an "Already Implemented" section, add a note: Closed by /fix-issues sync.

Step 5 — Commit & report

Commit updated tracker files.

Report:

Sync complete.
  Open issues: N
  Newly researched: M
  Tracker files updated: K
  Closed (verified fixed): J (#NNN, #NNN, ...)
  Likely fixed (needs human review): L (#NNN, #NNN)
  Gaps: [any GH issues not in any tracker]

Exit.

Plan (if `plan` is present)

Draft plans for issues previously skipped as "too complex for batch fix." Accepts optional auto — /fix-issues plan auto skips the selection gate and drafts plans for all found issues.

Run node scripts/skipped-issues.cjs --check-gh — this scans the ENTIRE SPRINT_REPORT.md across all sprints, extracts skipped issue numbers (including ranges like #148-#168), deduplicates against existing executable plans in plans/, and checks GitHub issue state. Output is JSON with each issue classified as needs-plan, has-plan, or closed.

Use the script output directly — do NOT manually grep SPRINT_REPORT.md.
Deduplicate — check plans/ for existing plans that already cover each issue. Also check whether the issue is still open on GitHub (gh issue view <N> --json state). Remove issues that already have a plan or are closed.

Present findings (unless auto):

Found N issues needing plans:

# Title Source
#142 Drag into subsystem Sprint 2026-03-17: Skipped — Too Complex
#363 Algebraic loop detection Sprint 2026-03-16: Remaining Open
...
Already have plans: #NNN, #NNN (skipped)
Already closed: #NNN (skipped)

Which issues should I draft plans for? (all / comma-separated numbers / none)

Wait for the user's selection before proceeding. If auto, skip this step and plan all of them.

For each selected issue, create a delegation requirement marker and then dispatch /draft-plan. The marker goes under fix-issues' own per-sprint subdir ($PIPELINE_ID) — the parent reconciles child fulfillment in its own scope:
```
MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
mkdir -p "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID"
printf 'skill: draft-plan\nparent: fix-issues\nissue: %s\ndate: %s\n' \
  "$ISSUE_NUMBER" "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/requires.draft-plan.$ISSUE_NUMBER"
```
Then dispatch /draft-plan with:
- The issue number and full body (gh issue view <N> --json body)
- Any research blurb from the tracker files
- Output path: plans/{issue-slug}.md
Report:
Plans drafted: N
- plans/foo-bar.md (#123) — [one-line summary]
- plans/baz-qux.md (#456) — [one-line summary] Already had plans: M (skipped) Closed issues: K (skipped) User declined: J
Exit. Plans are ready for /run-plan execution.

Phase 0 — Schedule (if `every` is present)

If $ARGUMENTS contains every <schedule>:

Parse the schedule — convert to a cron expression. The LLM interprets natural scheduling expressions.

For interval-based schedules (4h, 2h, 30m): use the CURRENT minute as the offset so the first fire is a full interval from now, not aligned to midnight. Check the current minute with date +%M:
- 4h at minute 9 → 9 */4 * * * (fires at :09 past every 4th hour)
- 2h at minute 15 → 15 */2 * * *
- 30m → */30 * * * * (no offset needed for sub-hour)
- 1h at minute 9 → 9 * * * *
For time-of-day schedules (day at 9am, weekday at 2pm): offset round minutes by a few to avoid API busy marks:
- day at 9am → 3 9 * * *
- day at 14:00 → 3 14 * * *
- weekday at 9am → 3 9 * * 1-5
Deduplicate — use CronList to list existing cron jobs. Use CronDelete to remove any whose prompt starts with Run /fix-issues (prevents duplicate schedules from accumulating).
Reconstruct the arguments for the cron prompt. Always include now in the cron prompt so each cron fire runs immediately AND re-registers itself (self-perpetuating). Note: this now is for the CRON's invocation, not the current invocation — the user controls whether THIS run executes immediately via their own now flag:
```
Run /fix-issues <N> [focus] auto every <schedule> now
```
Create the cron — use CronCreate:
- cron: the cron expression from step 1
- recurring: true
- prompt: the reconstructed command from step 3
Confirm — tell the user, including the estimated wall-clock time of the next run. Compute from the cron expression. Always show times in America/New_York (ET) — use TZ=America/New_York date for conversion, not the system timezone (which may be UTC). Example:

If now is present:

Fix-issues sprint scheduled every 4h. Running now. Next auto-sprint after this one: ~8:15 PM ET (cron ID XXXX).

If now is NOT present:

Fix-issues sprint scheduled every 4h. First run: ~4:15 PM ET (cron ID XXXX). Use /fix-issues next to check, /fix-issues stop to cancel.
If now is present: proceed to Phase 1 (run immediately). If now is NOT present: Exit. The cron will fire at the scheduled time. Do not run a sprint now.

End-of-sprint scheduling note: when a sprint finishes and a cron is active, always include the estimated next run time with timezone in the completion message. Example:

Sprint complete. Next auto-sprint in ~3h 45m (~11:30 PM ET, cron XXXX).

If every is NOT present, skip this phase entirely and proceed to Phase 1 (bare invocation always runs immediately).

Phase 1 — Preflight & Sync

Sprint tracking sentinel

When mode is sprint (N provided), construct the per-sprint unique $SPRINT_ID and $PIPELINE_ID FIRST (before any other tracking write), then create the pipeline sentinel:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
mkdir -p "$MAIN_ROOT/.zskills/tracking"

# Per-sprint unique ID (per Phase 1 design doc OQ3). Prevents concurrent
# fix-issues sessions from colliding on the literal "sprint" suffix. The
# ISSUE_TITLE slug is a human-readable tag; the UTC timestamp guarantees
# uniqueness across concurrent sprints on the same host.
ISSUE_TITLE_SLUG=$(printf '%s' "${ISSUE_TITLE:-sprint}" | tr -cd 'a-z0-9' | head -c 8)
[ -z "$ISSUE_TITLE_SLUG" ] && ISSUE_TITLE_SLUG="sprint"
SPRINT_ID="sprint-$(date -u +%Y%m%d-%H%M%S)-$ISSUE_TITLE_SLUG"
PIPELINE_ID="fix-issues.$SPRINT_ID"
PIPELINE_ID=$(bash scripts/sanitize-pipeline-id.sh "$PIPELINE_ID")
# Recover SPRINT_ID after sanitization (strip the "fix-issues." prefix).
SPRINT_ID="${PIPELINE_ID#fix-issues.}"
mkdir -p "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID"

if [ ! -f "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/pipeline.fix-issues.$SPRINT_ID" ]; then
  printf 'skill: fix-issues\nmode: sprint\ncount: %s\nfocus: %s\nstartedAt: %s\n' \
    "$N" "${FOCUS:-default}" "$(TZ=America/New_York date -Iseconds)" \
    > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/pipeline.fix-issues.$SPRINT_ID"
fi

Preflight checks (before doing anything else)

Before starting the sprint, check for stale state from a previous failed run:

In-progress git operation?
```
ls .git/CHERRY_PICK_HEAD .git/MERGE_HEAD .git/REBASE_HEAD 2>/dev/null
git status --porcelain | grep '^UU\|^AA\|^DD'
```
If either command produces output, the working tree has an unfinished cherry-pick, merge, or rebase — likely from a previous failed sprint. STOP. Invoke the Failure Protocol.

Note: normal uncommitted changes (modified plan files, logs) are expected and are NOT a reason to stop. Phase 6 stashes those before cherry-picking.
Stash stack?
```
git stash list
```
If there is a stash with message containing "pre-cherry-pick", a previous sprint's stash was never restored. STOP. Alert the user — they need to git stash pop or git stash drop before a new sprint can start safely.
Leftover sprint worktrees?
```
git worktree list
```
If worktrees from a previous sprint exist, warn the user. They may contain unapplied fixes. Do not remove them — just note their presence and continue.

If any preflight check fails, invoke the Failure Protocol (kill cron, alert user, write failure to report).

Sync

Fetch all open GitHub issues:

gh issue list --state open --limit 500 --json number,title,labels,createdAt

Run the sync script to find gaps between GitHub and plan files:
```
node ${CLAUDE_SKILL_DIR}/scripts/sync-issues.js
```

Run the stats script to see current distribution:

node ${CLAUDE_SKILL_DIR}/scripts/issue-stats.js

Update ALL issue trackers — scan plans/ for tracker files:
```
ls plans/*ISSUES*.md plans/ISSUES_PLAN.md 2>/dev/null
```
Ensure each tracker reflects current GitHub state. Add new issues to the appropriate tracker based on domain.
Identify gaps — any GH issues not tracked in any plan file? Add them to the appropriate tracker.
Research new issues — for each issue added in step 5 (or any issue lacking a research blurb in its tracker entry), dispatch research agents using the same workflow as the standalone sync command:
1. Read the full issue body (gh issue view <N>)
2. Search the codebase for the affected code
3. Write a concise research blurb (what's wrong, where, suggested approach)
4. Add the blurb to the appropriate tracker file
Without this step, Phase 2 prioritizes from bare titles and Phase 3 dispatches agents with no context — leading to misinterpretation. Past failure: #387 "reset button" was interpreted as "clear canvas" instead of "reset mappings to defaults" because only the title was read.

In auto mode, dispatch research agents in parallel (up to 3 at a time) and proceed after all complete. In interactive mode, present the research blurbs before moving to Phase 1b.

Phase 1b — Read Full Issue Bodies & Plan Context

Before prioritizing, gather full context for every candidate issue:

Fetch the issue body and comments from GitHub:

gh issue view <N> --json number,title,body,labels,comments

Fetch the research blurb from plan files:
```
grep -A 30 '#<N>' plans/*ISSUES*.md 2>/dev/null
```
Plan blurbs contain root cause analysis, affected files, suggested fixes, and effort estimates. This context was gathered when the issue was filed — don't waste time re-researching what's already documented.

Both steps are mandatory. Titles are often vague or misleading. The body and plan blurb together are the spec. You cannot prioritize or write accurate agent prompts without reading both.

For each candidate, note:

What the user actually described (not what the title implies)
Root cause and affected files (from plan blurb)
Repro steps if provided
Suggested fix approach (from plan blurb)
Context metadata (model name, browser, screen size)

Post-preflight tracking

After Phase 1 (preflight + sync + research) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.preflight"

Phase 2 — Prioritize

Present the next N issues to fix as a ranked table:

Priority	#	Title	Severity	Domain	Effort	Tracker

If a focus argument is provided, issues in that domain are boosted to the top, then the remaining slots filled by default priority.

Default ranking criteria (in order):

New issues not yet attempted (user feedback, recently filed)
Correctness defects (from issue trackers tagged as correctness)
Critical/high severity bugs
Quick wins (15 min – 1 hour)
Issues with clear repro steps
Test gaps (from issue trackers tagged as test quality)

Triage: vague, complex, or interrelated issues

While building the ranked list, classify each candidate:

Clear and doable — repro steps, expected behavior, affected files identified. Include in the sprint.
Too vague — no repro steps, no expected behavior, body is empty or just "it's broken." You don't know WHAT to fix.
- Interactive: flag it and ask the user for clarification
- Auto: skip it, report as "Skipped: insufficient context" in SPRINT_REPORT.md
Too complex — clear spec but would require 500+ lines, major refactoring, or architectural changes. Not a batch-fix item.
- Interactive: report "this needs /run-plan, not /fix-issues"
- Auto: skip it, report as "Skipped: too complex for batch fix"
- If plans/PLAN_INDEX.md exists, grep plan files for the issue number (e.g., #NNN). If a plan already covers this issue, note which plan in the skip reason. If no plan covers it, add to the skip note: "Consider /draft-plan for #NNN."

Group by dependency and file overlap

Before dispatching agents, check for interrelated issues:

Same root cause — if #100 and #101 are both caused by an off-by-one in Solver.js, group them for the same agent. One agent, one worktree, one fix closes both.
Same file — if #200 and #201 both need changes to Parser.js, group them for the same agent. Separate worktrees would produce conflicting cherry-picks.
Prerequisite relationship — if fixing #300 requires the fix from #299 to be in place, give both to the same agent in order.

Tell the agent when issues are related: "Issues #100 and #101 share root cause X in file Y — consider fixing them together with a single commit."

Present the list

Without auto: Wait for user approval of the list before proceeding. Include the grouping rationale so the user can adjust.
With auto: Present the ranked table for the record, then proceed immediately using the ranking criteria above.

If no actionable issues found

If ALL candidates are too vague, too complex, or already attempted:

Auto-sync before giving up. Run the full Sync workflow (Steps 1-5). In auto mode, auto-close issues with FIXED verdict (commit hash + tests — the same bar as interactive sync, just without the approval gate). LIKELY FIXED and UNCLEAR still require human judgment and are skipped. Then re-run Phase 1b and Phase 2 to re-evaluate the candidate pool. If actionable issues are now available, proceed to Phase 3 normally.

Only sync once per sprint. If still empty after, proceed to step 2.
If still no actionable issues after refresh:
- Write a minimal sprint section to SPRINT_REPORT.md: ## Sprint — YYYY-MM-DD HH:MM [UNFINALIZED] with "No actionable issues found (synced twice)" and the skip reasons.
- Do NOT kill the cron — new issues may be filed before the next run.
- After 3 consecutive empty runs, add a note: "3 consecutive runs with no actionable issues. Run /fix-issues stop if no new issues are expected." Do NOT auto-stop — that's the user's call.
- Exit. Skip Phases 3-6.

Post-prioritize tracking

After Phase 2 (prioritize) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\nissueCount: %d\n' "$(TZ=America/New_York date -Iseconds)" "$ISSUE_COUNT" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.prioritize"

Phase 3 — Execute (agent teams in worktrees)

Interrelated issues (same root cause or same files from Phase 2 grouping) share one agent and one worktree. Tell the agent which issues are grouped and why.
Unrelated issues get separate agents. Never batch unrelated hard issues into one agent — this caused a 4.5h bottleneck when one agent got 4 diverse issues sequentially.

Agent timeout: 1 hour. Note the dispatch time for each agent. If an agent hasn't returned after 1 hour, declare it failed:

Mark its issues as "Timed out" in SPRINT_REPORT.md
Issues stay open for the next sprint
The worktree is a cleanup artifact — do NOT auto-land late results
If the agent eventually returns, ignore it. Timed out = failed, period.

Agent dispatch prompts MUST include for each issue:

The verbatim issue body from Phase 1b (gh issue view). Do NOT paraphrase or summarize — include the full text the user wrote. Titles are often vague; the body is the spec. If the body is empty, say so explicitly.
The research blurb from issue tracker files (plans/*ISSUES*.md). These contain root cause analysis, affected files, suggested fixes, and effort estimates written when the issue was filed. Grep the tracker files for the issue number and include any matching section verbatim.

The agent should have everything it needs to understand the problem without re-researching from scratch. Missing context = wrong fix.

Declare pipeline ID early in execution (before any git operation). $PIPELINE_ID was constructed at the top of Phase 1 ("Sprint tracking sentinel") as fix-issues.$SPRINT_ID:

echo "ZSKILLS_PIPELINE_ID=$PIPELINE_ID"

Before dispatching each fix agent to its worktree, write .zskills-tracked:

printf '%s\n' "$PIPELINE_ID" > "<worktree-path>/.zskills-tracked"

The echo associates the orchestrator session with this pipeline (read by hook from transcript). The .zskills-tracked file associates each worktree agent.

Each agent follows this fix workflow:

Read the issue body (included in prompt) and relevant code
Reproduce the bug (unit test or manual)
Implement the fix
Write regression tests (unit and/or E2E as appropriate)
Run npm run test:all — all suites must pass
Agent verification via /manual-testing if UI files changed — use playwright-cli with real events, take screenshots as evidence. The pre-commit hook will BLOCK your commit if UI files are staged but playwright-cli wasn't used in the session. This is not optional.
Classify User Verify — if any UI/editor/styles files changed (check your project's UI directories), mark User Verify: NEEDED in the sprint report. The user must see UI changes before the issue can be closed. This is in ADDITION to your agent verification.
Commit in the worktree (one issue per commit, clean history)
Rebase onto current main before final commit:
```
git fetch origin main && git rebase origin/main
```
This ensures the commit contains only the agent's changes, not stale copies of files other agents already fixed on main. If rebase conflicts, abort (git rebase --abort) and proceed — Phase 6 cherry-pick verification will catch stale files via selective extraction.

PR mode (Phase 3)

When LANDING_MODE == pr, each issue gets its own named branch and worktree (one PR per issue, unlike /run-plan PR mode where all phases share one branch).

Differences from /run-plan PR mode:

Branch prefix is hardcoded fix/ (not config branch_prefix)
Branch name uses the issue number, not a plan slug
Worktree path uses fix-issue-NNN, not pr-<plan-slug>
One worktree per issue (not one per plan)

Branch naming: fix/issue-NNN where NNN is the GitHub issue number.

Worktree path: /tmp/<project-name>-fix-issue-NNN

ISSUE_NUM=42
BRANCH_NAME="fix/issue-${ISSUE_NUM}"
PROJECT_NAME=$(basename "$PROJECT_ROOT")
WORKTREE_PATH="/tmp/${PROJECT_NAME}-fix-issue-${ISSUE_NUM}"

# Prune stale worktree entries. If /tmp was cleared (container restart,
# codespace rebuild), git still has the old worktree registered in
# .git/worktrees/. `git worktree prune` cleans up entries whose directories
# no longer exist, so `git worktree add` won't fail with "already registered."
git worktree prune

# Orchestrator creates worktree manually -- NOT via isolation: "worktree"
if [ -d "$WORKTREE_PATH" ]; then
  echo "Resuming existing fix worktree at $WORKTREE_PATH"
else
  # Legitimate multi-phase PR-mode resume — opt into branch resume.
  ZSKILLS_ALLOW_BRANCH_RESUME=1 \
    bash scripts/worktree-add-safe.sh "$BRANCH_NAME" "$WORKTREE_PATH" main
fi

# Pipeline association -- agent commits are gated by .zskills-tracked
echo "$PIPELINE_ID" > "$WORKTREE_PATH/.zskills-tracked"

Post-execute tracking

After Phase 3 (execute) is complete — all agents have returned:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.execute"

Phase 4 — Review

Pre-verification tracking

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
mkdir -p "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID"
printf 'skill: verify-changes\nparent: fix-issues\nmode: sprint\ndate: %s\n' \
  "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/requires.verify-changes.$SPRINT_ID"

Dispatch protocol

This delegates the full review workflow (diff review, test coverage audit, test run, manual verification, fix & re-verify cycle) to a separate agent.

Report the review results to the user.

Post-verify tracking

After Phase 4 (verify) is complete — all verification agents have returned:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.verify"

Phase 5 — Write Sprint Report (BEFORE landing)

APPEND a new sprint section to SPRINT_REPORT.md BEFORE Phase 6 (landing). The report is a prerequisite for landing — if it's not written, Phase 6 does not execute.

If the file doesn't exist, create it with a # Sprint Report heading.

Report format — each sprint appends a section like this:

## Sprint — YYYY-MM-DD HH:MM [UNFINALIZED]

**Mode:** auto | interactive | **Focus:** <focus> | default

### Fixed
| # | Title | Worktree | Commit | Tests | Agent Verify | User Verify |
|---|-------|----------|--------|-------|-------------|-------------|
| #123 | Solver crash | wt-123 | abc1234 | 2 unit | PASS (tests) | N/A |
| #456 | Button offset | wt-456 | def5678 | 1 E2E | PASS (screenshot) | NEEDED |

**Agent Verify:** Did the agent test it? PASS (with method) or SKIPPED.
The pre-commit hook blocks commits without test evidence.

**User Verify:** Does the user need to see this? Mechanically classified:
if any UI/editor/styles files changed → `NEEDED`. Otherwise → `N/A`.
`/fix-report` Step 2
presents all `NEEDED` items for user review before closing.

### Skipped — Too Vague (need repro steps or clearer spec)
| # | Title | What's Missing |
|---|-------|----------------|

### Skipped — Too Complex (need /run-plan)
| # | Title | Why |
|---|-------|-----|

### Skipped — Cherry-Pick Conflict (will retry next sprint)
| # | Title | Conflict Details |
|---|-------|-----------------|
| #789 | Parser error | cherry-pick conflict on commit abc1234 |

### Not Fixed (agent attempted but failed)
| # | Title | Reason |
|---|-------|--------|

Post-report tracking

After Phase 5 (report) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.report"

Phase 6 — Land

Landing mode dispatch:

LANDING_MODE == cherry-pick — default path (below).
LANDING_MODE == pr — see "PR mode landing" subsection. One PR per fixed issue, with Fixes #NNN linking.
LANDING_MODE == direct — no-op: work was committed on main by the verification agent (no worktree isolation was used). Proceed to post-land tracking. Note: direct mode still requires the verification agent to commit — it just doesn't cherry-pick or push to a branch.
Without auto: Sprint complete. Output:

Sprint complete. Report written to SPRINT_REPORT.md. Run /fix-report to review fixes, land to main, and close issues.

All interactive landing, closing, and cleanup moves to /fix-report. /fix-issues is DONE after writing the report.
With auto: Auto-land verified fixes to main:
1. Try cherry-picking WITHOUT stashing first. Git allows cherry-picks on a dirty working tree as long as the cherry-picked files don't overlap with uncommitted changes. Other sessions may have uncommitted work in the tree — stashing captures THEIR changes too, and the pop can silently merge or lose them. Past failure: stash/pop cycle during cherry-pick wiped out another session's skill changes.
  
  If git refuses with "your local changes would be overwritten," the cherry-pick touches files with uncommitted changes. Handle with LLM-assisted merge:
  1. Note which files overlap
  2. Capture the pre-stash state of each overlapping file: git diff <file> — save/remember this output. It's your evidence of what the uncommitted changes were (possibly from another session).
  3. git stash -u -m "pre-cherry-pick stash"
  4. git cherry-pick <commit-hash>
  5. git stash apply (NOT pop — keep the stash as a recovery path)
  6. If stash apply produces conflict markers (<<<<<<<), resolve them — read both sides and combine. This is expected for overlaps.
  7. For every overlapping file, READ the result and compare against the pre-stash diff from step 2. Verify every changed line from the uncommitted changes is still present AND the cherry-pick's fix landed correctly. If the merge dropped changes, restore them.
  8. After verification, drop the stash: git stash drop
  9. If you genuinely can't reconcile (same lines, conflicting purposes), STOP and report to the user.
2. Verify main is clean before cherry-picking:
```
npm run test:all
```
  If main's tests are already failing, STOP. Invoke the Failure Protocol — do not cherry-pick on top of broken code. Report: "main is broken before cherry-pick. Fix main first."
3. Cherry-pick sequentially — one commit at a time, verify each succeeds before the next. Try without stash first (step 1). Only stash if git refuses due to file overlap.
4. If a cherry-pick conflicts: abort and skip that worktree's commits. If the worktree has multiple commits (grouped interrelated issues), skip ALL of them — they likely depend on each other.
```
git cherry-pick --abort
```
  Mark the issues as "Skipped: cherry-pick conflict" in SPRINT_REPORT.md. Continue cherry-picking from other worktrees. Do NOT invoke the Failure Protocol for skipped worktrees.
  
  The skipped issues stay open and will be picked up in the next sprint — by then the conflicting fix is on main, so the conflict resolves itself.
5. Extract logs and mark worktrees as landed — for each worktree whose commits were successfully cherry-picked: a. Copy unique session logs to main:
```
if [ -d "<worktree>/.claude/logs" ]; then
  for log in <worktree>/.claude/logs/*.md; do
    [ -f ".claude/logs/$(basename $log)" ] || cp "$log" .claude/logs/
  done
fi
```
  b. Write .landed marker (atomic):
```
cat <<LANDED | bash scripts/write-landed.sh "<worktree>"
status: full
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
commits:
  <list of cherry-picked commit hashes and messages>
LANDED
```
  c. For tiers that were SKIPPED (conflict), write partial marker:
```
cat <<LANDED | bash scripts/write-landed.sh "<worktree>"
status: partial
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
landed: <hashes that did land, if any>
skipped: <hashes that conflicted>
reason: cherry-pick conflict
LANDED
```
6. Commit extracted logs:
```
git add .claude/logs/
git commit -m "chore: session logs from fix-issues sprint"
```
7. Restore stash if one was created:
```
git stash pop
```
8. Run tests after all cherry-picks land:
```
npm run test:all
```
  If tests fail, invoke the Failure Protocol — do not leave broken code on main with the cron still running.
9. Update SPRINT_REPORT.md — mark which fixes were landed (add a Landed column or update status).
10. Auto-remove fully landed worktrees — for each worktree with status: full in .landed:
```
# Logs already extracted in step 5a. Double-check for stragglers:
if [ -d "<worktree>/.claude/logs" ]; then
  for log in <worktree>/.claude/logs/*.md; do
    [ -f ".claude/logs/$(basename "$log")" ] || cp "$log" .claude/logs/
  done
fi

# Check for real uncommitted work (not artifacts)
DIRTY=$(git -C "<worktree>" diff --name-only HEAD)
UNTRACKED=$(git -C "<worktree>" status --porcelain | \
  grep -v '\.landed\|\.worktreepurpose\|\.test-results\|\.playwright\|node_modules')

if [ -z "$DIRTY" ] && [ -z "$UNTRACKED" ]; then
  rm -f "<worktree>/.landed" "<worktree>/.worktreepurpose"
  git worktree remove "<worktree>"
  git branch -d "<branch>" 2>/dev/null
else
  echo "Worktree <name> not auto-removed: uncommitted work found"
fi
```
  Skip removal for worktrees with status: partial — those have unapplied commits that need attention.
11. Done. Closing GH issues and updating trackers are still /fix-report actions — even in auto mode.

PR mode landing

Loop over every fixed issue (and any grouped issue worktrees from Phase 2). $FIXED_ISSUES is the list of issue numbers whose worktrees have verified commits on fix/issue-NNN.

Rebase before push (same pattern as /run-plan PR mode rebase point 2, but per issue — fix-issues is single-phase per issue, so only one rebase point is needed):

cd "$WORKTREE_PATH"
git fetch origin main
PRE_REBASE=$(git rev-parse HEAD)
git rebase origin/main
if [ $? -ne 0 ]; then
  # Abort and mark this issue as conflict. Continue to the next issue.
  if [ -d "$(git rev-parse --git-dir)/rebase-merge" ] || \
     [ -d "$(git rev-parse --git-dir)/rebase-apply" ]; then
    git rebase --abort
  fi
  echo "REBASE CONFLICT for issue #$ISSUE_NUM."
  cat <<LANDED | bash scripts/write-landed.sh "$WORKTREE_PATH"
status: conflict
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
method: pr
branch: $BRANCH_NAME
issue: $ISSUE_NUM
reason: rebase-conflict
LANDED
  continue  # Move to next issue
fi
if [ "$(git rev-parse HEAD)" != "$PRE_REBASE" ]; then
  echo "Main moved -- re-verifying issue #$ISSUE_NUM before push..."
  # Dispatch /verify-changes worktree re-verification.
  # Agent prompt includes "FIRST: cd $WORKTREE_PATH".
  # Re-verification has its own fix cycle (max 2 attempts), independent
  # of the CI fix budget. If re-verification fails after its own max
  # attempts, mark the issue as pr-failed and move on.
fi

Push + PR creation (per issue):

for issue in "${FIXED_ISSUES[@]}"; do
  ISSUE_NUM="$issue"
  BRANCH_NAME="fix/issue-${ISSUE_NUM}"
  PROJECT_NAME=$(basename "$PROJECT_ROOT")
  WORKTREE_PATH="/tmp/${PROJECT_NAME}-fix-issue-${ISSUE_NUM}"

  # Fetch issue title for the PR title
  ISSUE_TITLE=$(gh issue view "$ISSUE_NUM" --json title --jq '.title' 2>/dev/null || echo "Issue $ISSUE_NUM")

  cd "$WORKTREE_PATH"

  # Push (new or update)
  if git ls-remote --heads origin "$BRANCH_NAME" | grep -q "$BRANCH_NAME"; then
    echo "Remote branch $BRANCH_NAME already exists. Pushing updates."
    git push origin "$BRANCH_NAME"
  else
    git push -u origin "$BRANCH_NAME"
  fi

  # Existing PR? Update, don't duplicate.
  EXISTING_PR=$(gh pr list --head "$BRANCH_NAME" --json number --jq '.[0].number' 2>/dev/null)
  if [ -n "$EXISTING_PR" ]; then
    PR_URL=$(gh pr view "$EXISTING_PR" --json url --jq '.url')
    PR_NUMBER="$EXISTING_PR"
  else
    PR_URL=$(gh pr create \
      --title "Fix #${ISSUE_NUM}: ${ISSUE_TITLE}" \
      --body "$(cat <<EOF
Fixes #${ISSUE_NUM}

## Changes
${CHANGE_SUMMARY}

## Test plan
- [ ] Verify the fix resolves the original issue
- [ ] All existing tests pass
EOF
)" \
      --base main \
      --head "$BRANCH_NAME")
    if [ -n "$PR_URL" ]; then
      PR_NUMBER=$(gh pr view --json number --jq '.number')
    fi
  fi

  # If PR creation failed, write pr-failed marker and continue.
  if [ -z "$PR_URL" ]; then
    echo "WARNING: PR creation failed for issue #$ISSUE_NUM. Branch pushed but PR not created."
    cat <<LANDED | bash scripts/write-landed.sh "$WORKTREE_PATH"
status: pr-failed
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
method: pr
branch: $BRANCH_NAME
issue: $ISSUE_NUM
pr:
commits: $(git log main.."$BRANCH_NAME" --format='%h' | tr '\n' ' ')
LANDED
    continue
  fi

  # --- CI check + auto-merge: same pattern as /run-plan 3b-iii ---
  # See skills/run-plan/SKILL.md "PR mode landing" for the canonical
  # implementation: config re-read, pre-check retry, polling, fix cycle,
  # auto-merge, .landed upgrade.
  #
  # Differences from /run-plan PR mode:
  #   - source: "fix-issues" (not "run-plan")
  #   - .landed marker includes `issue: $ISSUE_NUM`
  #   - `timeout 300` per issue (NOT 600) to avoid serial accumulation
  #     across N issues. If CI doesn't resolve in 5 min for a given issue,
  #     write status: pr-ready and move on. The next cron turn or the
  #     user re-checks.
  #
  # Parallel optimization (future): if the orchestrator can dispatch
  # sub-agents, each issue's CI polling can run in parallel. Not required
  # for initial implementation.

  # --- .landed marker (per issue) ---
  # $LANDED_STATUS, $CI_STATUS, $PR_STATE come from the CI/auto-merge block.
  cat <<LANDED | bash scripts/write-landed.sh "$WORKTREE_PATH"
status: $LANDED_STATUS
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
method: pr
branch: $BRANCH_NAME
pr: $PR_URL
ci: $CI_STATUS
pr_state: $PR_STATE
issue: $ISSUE_NUM
commits: $(git log main.."$BRANCH_NAME" --format='%h' | tr '\n' ' ')
LANDED

  echo "Issue #$ISSUE_NUM -> PR: $PR_URL (status: $LANDED_STATUS)"

  # Cleanup on merge: same as /run-plan PR mode -- if status is `landed`
  # (PR merged), call land-phase.sh to remove the worktree.
  if [ "$LANDED_STATUS" = "landed" ]; then
    bash scripts/land-phase.sh "$WORKTREE_PATH"
  fi
done

.landed status values for PR mode (same as /run-plan):

Scenario	status	method	ci	pr_state
PR merged (auto-merge)	`landed`	`pr`	`pass`/`none`/`skipped`	`MERGED`
PR open, CI passed, awaiting review	`pr-ready`	`pr`	`pass`/`none`/`skipped`	`OPEN`
PR open, CI timed out (still running)	`pr-ready`	`pr`	`pending`	`OPEN`
PR open, CI failing after max attempts	`pr-ci-failing`	`pr`	`fail`	`OPEN`
Branch pushed, PR creation failed	`pr-failed`	`pr`	(not set)	(not set)
Rebase conflict	`conflict`	`pr`	(not set)	(not set)

In all PR mode markers, the issue: field records which GitHub issue the branch resolves. /fix-report reads this field to group PR URLs with issue numbers in the sprint summary.

Post-land tracking

After Phase 6 (land) is complete:

MAIN_ROOT=$(cd "$(git rev-parse --git-common-dir)/.." && pwd)
printf 'completed: %s\n' "$(TZ=America/New_York date -Iseconds)" \
  > "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/step.fix-issues.$SPRINT_ID.land"

After the sprint completes (whether all issues landed or the sprint ended), clean up the sentinel:

rm -f "$MAIN_ROOT/.zskills/tracking/$PIPELINE_ID/pipeline.fix-issues.$SPRINT_ID"

Also remove .zskills-tracked from each worktree that was used.

Failure Protocol

1. Kill the cron FIRST

CronList → find the /fix-issues job ID → CronDelete

Do this BEFORE any cleanup or reporting. Even if you're about to fix the problem, kill the cron. The user can restart it after reviewing.

2. Restore the working tree

If a cherry-pick is in a conflicted state:

git cherry-pick --abort

If a stash was created during Phase 6 auto-land:

git stash pop

Stash pop conflicts. Stash preserved (contains untracked files). Run git stash show to inspect, then git stash pop manually.

Never destroy work to clean up. It's always better to STOP with a messy state than to lose files trying to clean up.

3. Write the failure to SPRINT_REPORT.md

Create the file if it doesn't exist (preflight failures happen before Phase 5 creates it). If it already exists, add the failure section immediately after the # Sprint Report heading.

Add a ## Sprint Failed section at the top of the report:

## Sprint Failed — YYYY-MM-DD HH:MM

**Phase:** [which phase failed]
**Error:** [what went wrong]
**State:**
- Cherry-picks landed before failure: [list or "none"]
- Stash restored: yes/no
- Worktrees with changes: [list]
- Cron killed: yes (was job ID XXXX)

**To resume:** Review the state above, then either:
- Run `/fix-report` to finalize what succeeded
- Run `/fix-issues ... every` to restart the cron after resolving

4. Alert the user

Output a clear, prominent message:

⚠ SPRINT FAILED — cron stopped

Phase N failed: [one-line reason]
[specific error details]

What happened:
  - [N] fixes were in worktrees, [M] were cherry-picked to main before failure
  - Stash was [restored / not needed]
  - Cron job [ID] has been CANCELLED — no more auto-runs until you restart

Working tree is clean. See SPRINT_REPORT.md for full details.
To restart: /fix-issues N auto every SCHEDULE now
To cancel: /fix-issues stop

Do not bury the failure in normal output. The user needs to see immediately that something broke, the cron is stopped, and what state was left behind.

When to trigger

Invoke this protocol for ANY of these:

npm run test:all fails after cherry-picks are landed (Phase 6 step 8) Note: cherry-pick CONFLICTS are handled by skip-and-continue (Phase 6 step 4), NOT the Failure Protocol. The protocol is only for test failures and unrecoverable errors.
The sprint globally produces 0 fixes (every agent failed or returned no commits) — note: this means ALL agents, not a single agent failing
GitHub API errors that prevent issue fetching
Preflight checks detect stale state (conflict markers, orphaned stash)
Any unrecoverable error that stops the sprint from completing normally

Do NOT invoke for:

Individual agent test failures in worktrees (those are reported in the sprint report as "Not Fixed" — the sprint continues with remaining fixes)
Warnings or non-blocking issues
Pre-existing test failures unrelated to the sprint

For failed/abandoned worktrees: when an agent returns no commits, crashes, or times out, the ORCHESTRATOR (not the failed agent) writes a failure marker on the worktree:

cat <<LANDED | bash scripts/write-landed.sh "<worktree>"
status: failed
date: $(TZ=America/New_York date -Iseconds)
source: fix-issues
issues: <issue numbers attempted>
reason: <agent returned no commits / agent crashed / tests failed>
LANDED

This ensures /fix-report can distinguish failed worktrees from active ones. The issues stay open for the next sprint.

Key Rules

Worktrees only — all fixes happen in isolated worktrees, never in the main working tree.
The verification agent commits after passing tests — the implementation agent does not commit. This satisfies the hook's test gate.
Never cherry-pick to main without permission — unless auto flag is set, in which case the user has pre-approved autonomous landing.
In auto mode, skip conflicting cherry-picks — abort the conflict, skip all commits from that worktree (grouped issues depend on each other), mark as "Skipped: conflict" in the report, and continue landing from other worktrees. The skipped issues self-heal next sprint.
Always write SPRINT_REPORT.md — it's the handoff to /fix-report.
Never close GH issues, update trackers, or remove worktrees — that's /fix-report's job.
One issue per commit — clean git history in worktrees.
npm run test:all before every commit — not just npm test.
Never weaken tests — fix the code, not the test. Do not loosen tolerances, skip assertions, or remove test cases.
Never defer the hard parts — finish all phases of the plan. Do not stop after the easy part and call remaining work "future phases."
Protect untracked files — before stash/cherry-pick/merge, inventory untracked files (git status -s | grep '^??'). Use git stash -u or save them first.
every implies auto — scheduling only makes sense for autonomous runs. If every is present but auto is not, treat it as if auto was set.
Deduplicate crons — always remove existing /fix-issues crons before creating a new one. Never let duplicate schedules accumulate.
Crons are session-scoped — they expire when the session dies. Tell the user to re-run /fix-issues ... every to restart scheduling.
Kill the cron on failure — if anything in the sprint fails unrecoverably, the FIRST action is CronDelete. A broken sprint + live cron = the next run stomps on the bad state. See the Failure Protocol for the full sequence.
Read every issue body before acting — gh issue view <N> is mandatory in Phase 1b. Titles are often vague or misleading. The body is the spec. Never paraphrase — include verbatim issue text in agent dispatch prompts. Past failure: #387 title "reset button" was interpreted as "clear canvas" instead of "reset mappings to defaults" because only the title was read.
Ultrathink — use careful, thorough reasoning. Read code, understand what changed and why, verify correctness.

#	Title	Source
#142	Drag into subsystem	Sprint 2026-03-17: Skipped — Too Complex
#363	Algebraic loop detection	Sprint 2026-03-16: Remaining Open
...
Already have plans: #NNN, #NNN (skipped)
Already closed: #NNN (skipped)

fix-issues

More from this repository

More from this repository

/fix-issues N [focus] [auto] [every SCHEDULE] [now] | sync | plan [auto] | stop | next — Batch Bug-Fixing Sprint

Arguments

Now (standalone — no N provided)

Next (if next is present)

Stop (if stop is present)

Sync (if sync is present)

Step 1 — Fetch & update trackers

Step 2 — Research & verify

Step 3 — Present findings

Step 4 — Close approved issues on GitHub

Step 5 — Commit & report

Plan (if plan is present)

Phase 0 — Schedule (if every is present)

Phase 1 — Preflight & Sync

Sprint tracking sentinel

Preflight checks (before doing anything else)

Sync

Phase 1b — Read Full Issue Bodies & Plan Context

Post-preflight tracking

Phase 2 — Prioritize

Triage: vague, complex, or interrelated issues

Group by dependency and file overlap

Present the list

If no actionable issues found

Post-prioritize tracking

Phase 3 — Execute (agent teams in worktrees)

PR mode (Phase 3)

Post-execute tracking

Phase 4 — Review

Pre-verification tracking

Dispatch protocol

Post-verify tracking

Phase 5 — Write Sprint Report (BEFORE landing)

Post-report tracking

Phase 6 — Land

PR mode landing

Post-land tracking

Failure Protocol

1. Kill the cron FIRST

2. Restore the working tree

3. Write the failure to SPRINT_REPORT.md

4. Alert the user

When to trigger

Key Rules

/fix-issues N [focus] [auto] [every SCHEDULE] [now] | sync | plan [auto] | stop | next — Batch Bug-Fixing Sprint

Arguments

Now (standalone — no N provided)

Next (if next is present)

Stop (if stop is present)

Sync (if sync is present)

Step 1 — Fetch & update trackers

Step 2 — Research & verify

Step 3 — Present findings

Step 4 — Close approved issues on GitHub

Step 5 — Commit & report

Plan (if plan is present)

Phase 0 — Schedule (if every is present)

Phase 1 — Preflight & Sync

Sprint tracking sentinel

Preflight checks (before doing anything else)

Sync

Phase 1b — Read Full Issue Bodies & Plan Context

Post-preflight tracking

Phase 2 — Prioritize

Triage: vague, complex, or interrelated issues

Group by dependency and file overlap

Present the list

If no actionable issues found

Post-prioritize tracking

Phase 3 — Execute (agent teams in worktrees)

PR mode (Phase 3)

Post-execute tracking

Phase 4 — Review

Pre-verification tracking

Dispatch protocol

Post-verify tracking

Phase 5 — Write Sprint Report (BEFORE landing)

Next (if `next` is present)

Stop (if `stop` is present)

Sync (if `sync` is present)

Plan (if `plan` is present)

Phase 0 — Schedule (if `every` is present)

Next (if `next` is present)

Stop (if `stop` is present)

Sync (if `sync` is present)

Plan (if `plan` is present)

Phase 0 — Schedule (if `every` is present)