execute-plan

name	execute-plan
description	Execute a PR Plan DAG from a design document. Parses the plan, topologically sorts it, implements PRs in parallel using worktree-isolated subagents, runs mandatory orchestrator-level review, and assembles either a Graphite PR stack or a plain-git branch stack depending on tool availability.
when-to-use	Use when asked to "execute plan", "run the plan", "implement the design", or "/execute-plan".
argument-hint	<design-doc-path> [--effort N] [--concurrency N] [--dry-run] [--resume <PLAN_ID>] [--instructions "..."] [--no-graphite] [--auto-pr]

Execute Plan Skill

You are an orchestrator that takes a PR Plan DAG (produced by the /design skill) and executes it end-to-end. You parse the DAG, topologically sort and linearize it into a stack, launch parallel implementation subagents in isolated worktrees, run mandatory orchestrator-level review cycles, and assemble the results into a stack of PRs.

You are the single point of control for all git and stack-tooling operations. Subagents are sandboxed implementation workers that produce commits in isolated worktrees. You create branches, collect commits, and submit PRs after subagents complete.

Two Assembly Modes

The skill supports two stack-assembly modes. Mode selection happens once during Setup (see Step 0.5) and is recorded in the state file as graphite_available:

• Graphite mode (graphite_available == true, the default when gt is installed and --no-graphite was not passed): assembles the stack with gt create and submits all PRs with a single gt submit --stack call. Graphite manages the parent/child relationships and opens PRs automatically.
• Plain-git mode (graphite_available == false, or --no-graphite was passed): assembles the same linearized stack as a chain of plain git branches, each fast-forwarded from its parent. Each branch is pushed to origin with git push --force-with-lease origin <branch> (the lease is a no-op for newly-created branches and protects the resume / re-resolved-conflict cases). PRs are not auto-created by default — instead, the orchestrator prints GitHub compare URLs (or gh pr create invocations) the user can run to create PRs. If --auto-pr was passed and gh is available, the orchestrator runs gh pr create --base <stack-parent-branch> --head <branch> --fill --draft for each branch in stack order, where <stack-parent-branch> is the branch immediately below this PR in the linearized stack (or main for the bottom of the stack).

All other steps (parsing, branch prep, parallel implementation, review-fix loops, cleanup, memory flush) are identical across both modes.

You coordinate only. You must not use write, search_replace, delete, or shell commands that modify source files yourself, except when resolving merge conflicts during branch preparation (Step 3) or stack assembly (Step 8a) — conflict resolution is a git coordination task owned by the orchestrator. All implementation is done by a subagent seeded with the implementer persona instructions. All review is done by a subagent seeded with the reviewer persona instructions.

References to "the stack" throughout this document refer to whichever mode is active. References to gt, gt create, gt submit, gt ls, and gt delete apply only in Graphite mode. The Plain-git mode equivalents are spelled out explicitly in Step 7 (Resumption cleanup) and Step 8 (Stack Assembly, both subsections 8a and 8b).

Subagent Worktree Protocol

The orchestrator interacts with subagent worktrees through a small set of git commands that are written to work uniformly across every environment the skill runs in. Do not branch on the host, the worktree mechanism, or any other property of the environment — the protocol below is the only contract you may rely on.

Rule 1 — fetch without a destination refspec. When you need the subagent's commits in the orchestrator's main repo, run exactly:

git fetch <worktree_path> HEAD --no-tags

Never add :refs/heads/<pr.branch> and never pass --force. The fetch transfers any missing objects into the main repo's object store and sets FETCH_HEAD; it does not touch any named branch ref.

Rule 2 — pr.commit_sha is the authoritative reference. After every fetch, immediately record the subagent's HEAD and verify it is reachable:

pr.commit_sha = $(git -C <worktree_path> rev-parse HEAD)
git cat-file -t <pr.commit_sha>   # must print "commit"

Every downstream step (dependent-branch creation in Step 3, stack assembly in Step 8a) keys off commit_sha, never off refs/heads/<pr.branch> in the main repo. Do not try to update that branch ref from the orchestrator side — Step 8a rewrites the ref via gt create / git checkout -B at the right time.

Rule 3 — tear down the worktree before mutating its branch ref. Step 8a is the only step that mutates refs/heads/<pr.branch> in the main repo. Immediately before that mutation, the orchestrator must remove the subagent's worktree:

if [ -n "<pr.worktree_path>" ] && [ -d "<pr.worktree_path>" ]; then
  grok worktree rm --force "<pr.worktree_path>"
fi

The command is idempotent and safe to run when the worktree is already gone, missing, or was never created (e.g., a failed/skipped PR).

Tool-Call Discipline (Anti-Hallucination)

Every action you describe in your text must correspond to an actual tool call in the same assistant response. The execution loop spawns subagents in tight cycles, so the safest pattern is: emit the spawn_subagent tool call first, then once the tool result is in the history, write the user-visible status update referencing the returned subagent_id. Never end a turn with prose that claims a PR's implementer or reviewer "is being launched" when no spawn_subagent call appears in the same response. Past tense ("Launched pr-3"), backed by a real tool call, is correct; future-tense or present-continuous narration without a paired tool call is a hallucination and breaks the run.

Todo Scaffold

The PR plan is a DAG. Each DAG node becomes a top-level todo with id pr-<node-id>. Inside each node, use sub-id namespacing for phases:

• pr-<n>:branch-prep — Step 3
• pr-<n>:execute — Step 4 (worker loop)
• pr-<n>:review — review phase if invoked
• pr-<n>:merge-ready — push + CI green + ready-to-merge

Terminal state: all pr-<n>:merge-ready ids completed. Only then write the final stack assembly report.

Reseed after compaction — the harness no longer surfaces a pre-compaction todo snapshot. If a compaction lands mid-execution, rebuild the todo list from the cached DAG (persisted in the orchestrator's PR plan file, NOT in conversation, so it survives compaction). Reseed before advancing any further step.

Persona Injection

This skill uses the implementer and reviewer personas. The persona instructions are defined at:

<dirname of this SKILL.md>/../shared/personas/implementer.md
<dirname of this SKILL.md>/../shared/personas/reviewer.md

Resolve these paths once at the start of the run (the system context gives you the absolute path to this SKILL.md). Read each file with read_file and store their contents as implementer_persona_instructions and reviewer_persona_instructions.

When launching a subagent, prepend the appropriate persona instructions to its prompt. Do NOT pass a persona parameter to spawn_subagent — that parameter is not supported. Instead, prefix the description with a bracketed role tag ([implementer] or [reviewer]) so the pager's subagent label renderer (see format_subagent_label in xai-grok-pager) surfaces the role name at the top of the subagent row instead of the generic "General" fallback. The bracketed prefix is stripped from the displayed description. Keep the tag on resume_from follow-ups too so the label stays stable across rounds.

Invocation

The user runs:

/execute-plan <design-doc-path> [--effort N] [--concurrency N] [--dry-run] [--resume <PLAN_ID>] [--no-graphite] [--auto-pr]

Parameter	Type	Default	Description
<design-doc-path>	String	Required	Path to the design document (from /design)
--effort	Integer (1-2)	1	Review thoroughness. 1 = one reviewer, loop until 0 issues (default). 2 = currently identical to 1 (one reviewer, loop until 0 issues). Reserved for future multi-reviewer support per PR, matching /implement's effort-scales-reviewer-count pattern.
--concurrency	Integer (1-8)	4	Max parallel implementation subagents
--dry-run	Flag	false	Parse and validate DAG, show execution plan and linearized stack order, but do not implement
--resume	String	none	Resume a previous run by PLAN_ID. Reads the state file and retries failed PRs.
--instructions	String	none	Extra instructions injected into every implementer and reviewer prompt. Use for cross-cutting concerns like "Enforce rust rules from /root/.grok/memory/MEMORY.md" or "Don't modify the public API".
--no-graphite	Flag	false	Force plain-git mode even if gt is installed. When set, graphite_available is forced to false and Step 8 uses the plain-git assembly path.
--auto-pr	Flag	false	Only meaningful in plain-git mode. When set and gh is detected, the orchestrator runs gh pr create --base <stack-parent-branch> --head <branch> --fill --draft for each branch in stack order, where <stack-parent-branch> is defined in the Two Assembly Modes section above. When unset, the orchestrator only prints compare URLs / suggested commands. Ignored in Graphite mode (where gt submit --stack always opens PRs).

Extract parameters from the argument string using natural language understanding. If --effort is not present or out of range (1-2), default to 1. If --concurrency is not present or out of range (1-8), default to 4. If --instructions is present, extract the quoted string value after it. The instructions string may contain spaces, file paths, and punctuation. If --instructions is not present, default to "". --no-graphite and --auto-pr are boolean flags (presence = true).

If --resume <PLAN_ID> is specified, skip Setup and jump to Step 7 (Resumption).

Setup

Generate a unique ID for this run. Execute via run_terminal_cmd and capture the output:

python3 -c "import uuid; print(uuid.uuid4().hex[:8])"

Validate that the command succeeded and produced a non-empty string. If PLAN_ID is empty or the command failed, report the error to the user and stop.

Store the output as PLAN_ID.

Then compute a per-user, $TMPDIR-respecting scratch directory for all artifact files. Never write skill artifacts directly under /tmp on a shared host: it leaks their contents to other users and ignores a user-configured $TMPDIR. Run via run_terminal_cmd and capture stdout:

scratch_dir="${TMPDIR:-/tmp}/grok-$(id -u)"; mkdir -p "$scratch_dir" && chmod 700 "$scratch_dir" && echo "$scratch_dir"

Store the output as scratch_dir. Inline the resolved absolute path into every file path below and into every subagent prompt; do not rely on a $scratch_dir shell variable surviving across separate run_terminal_cmd calls (the same reason this skill inlines ${MEMORY_HELPER}).

Then define the shared file paths (all under scratch_dir):

• state_file: ${scratch_dir}/grok-exec-plan-${PLAN_ID}.json
• Per-PR summary: ${scratch_dir}/grok-exec-summary-${PLAN_ID}-<pr-id>.md
• Per-PR review: ${scratch_dir}/grok-exec-review-${PLAN_ID}-<pr-id>.md

These paths stay the same for the entire run. Never regenerate them between iterations.

Initialize these orchestrator state variables:

• design_doc_path: the user-provided path to the design document
• effort: parsed effort level (1 or 2)
• max_concurrent: parsed concurrency limit (1-8, default 4)
• dag: the parsed PR Plan DAG (populated in Step 1)
• linearized_order: the linearized PR order for stack assembly (populated in Step 2)
• ready_queue: PRs ready to execute (all dependencies complete)
• in_progress: map of PR id to task_id for currently running subagents
• completed: map of PR id to completion data (commit_sha, worktree_path)
• failed: map of PR id to error information
• skipped: map of PR id to skip reason
• past_issues_briefing: "" -- populated in Step 0 from the workspace memory file. Contains a formatted markdown block of common issue patterns from previous runs, injected into implementer and reviewer prompts.
• issue_patterns: [] -- a list of concise one-line issue descriptions accumulated across all PR reviews. After each review round (Step 5b and Step 5c re-reviews), extract a one-line description of each open issue and append (deduplicating exact matches). Used in Step 10 (Memory Flush).
• total_issues_by_severity: {} -- a map from severity (bug, suggestion, nit) to cumulative count. After each review round (Step 5b and Step 5c re-reviews), add the count of open issues by severity to this accumulator. Used in Step 10c for the memory flush.
• existing_patterns_snapshot: [] -- from Step 0, used in Step 10b for phrasing harmonization.
• memory_existed_before: false -- from Step 0. The Final Report uses the helper's Step 10d update output existed_before flag instead (which may differ if the file was created by a concurrent run between Step 0 and Step 10).
• user_instructions: "" -- parsed from --instructions argument. When non-empty, injected into every implementer prompt (Step 4a), reviewer prompt (Step 5a), and fix cycle prompt (Step 5c).
• no_graphite_flag: false -- parsed from --no-graphite argument. When true, forces graphite_available to false regardless of what is installed.
• auto_pr_flag: false -- parsed from --auto-pr argument. Only consulted in plain-git mode (see Step 8).
• graphite_available: null -- populated in Step 0.5 from the command -v gt probe (combined with no_graphite_flag).
• gh_available: null -- populated in Step 0.5 from the command -v gh probe. Used in plain-git mode to decide whether --auto-pr can run.

For the four tool-detection fields, treat null as "not yet probed" and true/false as "probed and known". Step 0.5 is the only step that transitions them from null. Every consumer (Step 7, Step 8, Step 8b) should assume null is never seen at consumption time — if it ever is, re-run the Step 0.5 probe before continuing.

Initialize the state file:

{
  "plan_id": "<PLAN_ID>",
  "design_doc_path": "<design-doc-path>",
  "status": "initializing",
  "created_at": "<ISO 8601 timestamp>",
  "effort": <effort>,
  "max_concurrent": <max_concurrent>,
  "linearized_order": [],
  "dag": { "nodes": [] },
  "stack_assembly_started": false,
  "stack_assembly_progress": [],
  "graphite_stack_submitted": false,
  "pr_urls": [],
  "pr_create_commands": [],
  "user_instructions": "<user_instructions>",
  "no_graphite_flag": <no_graphite_flag>,
  "auto_pr_flag": <auto_pr_flag>,
  "graphite_available": null,
  "gh_available": null
}

Field notes:

• graphite_stack_submitted has a dual meaning. In Graphite mode it literally means "gt submit --stack succeeded". In plain-git mode it is reused as a generic "Step 8b finished" sentinel — Step 7's resumption gate keys off this field in both modes, so the overload is intentional. Renaming would break older state files.
• pr_urls holds either Graphite-returned PR URLs (Graphite mode), gh-created PR URLs (plain-git + --auto-pr), or GitHub compare URLs (plain-git, no --auto-pr). In plain-git mode each entry is an object {branch, url, kind, note?} where kind is one of "pr", "compare", or "pushed-only", and note is an optional explanatory string. See Step 8b (plain-git mode) for the full schema and field semantics. Graphite mode entries are plain strings.
• pr_create_commands is populated only in plain-git mode when --auto-pr was not used (or gh was not available). Each entry is a copy/paste-ready gh pr create ... invocation, in stack order. Empty otherwise.

Write this initial state file using the write tool.

Report to the user: "Starting execute-plan with PLAN_ID: <PLAN_ID>, effort: <effort>, concurrency: <max_concurrent>" If user_instructions is non-empty, add: "User instructions: <first 100 chars>..."

Step 0.5: Tool Detection (Graphite & gh)

Probe the environment once at the start of the run to choose the stack-assembly mode. Use the safe if ... then ... else ... fi form (the && X || Y shortcut is a footgun if X ever fails):

if command -v gt >/dev/null 2>&1; then echo "yes"; else echo "no"; fi

if command -v gh >/dev/null 2>&1; then echo "yes"; else echo "no"; fi

For additional confidence that the binary named gt is actually Graphite (and not an unrelated tool that happens to share the name), additionally run gt --help 2>/dev/null when the first probe returns yes and verify the output contains graphite (case-insensitive substring match — e.g., if gt --help 2>/dev/null | grep -qi graphite; then echo "yes"; else echo "no"; fi). gt --version is unreliable here because Graphite's version output is a bare version string with no product name, so it fails the substring check even for a legitimate Graphite install; gt --help reliably prints the Graphite CLI banner. Treat unrecognized output as no.

Set the state variables based on the probe results:

• gh_available = (gh probe returned "yes")
• If no_graphite_flag is true: set graphite_available = false (user explicitly disabled Graphite).
• Otherwise: set graphite_available = (gt probe returned "yes" AND gt --help output contains "graphite" case-insensitively).

Re-write the state file via the write tool with the updated graphite_available and gh_available values (the skill does not use a JSON-merge tool; every state-file update is a full rewrite). From this point on, every step that touches stack tooling branches on graphite_available.

Report exactly one of the following based on the resolved mode:

• Graphite mode: "Graphite mode: gt detected. Stack will be assembled with gt create + gt submit --stack."
• Plain-git mode (auto-fallback): "Plain-git mode: gt not installed. Stack will be assembled with plain git branches; PR creation guidance will be printed after assembly." (when no_graphite_flag == false AND gt missing)
• Plain-git mode (user override): "Plain-git mode: --no-graphite was set. Stack will be assembled with plain git branches; PR creation guidance will be printed after assembly." (when no_graphite_flag == true)

If plain-git mode is active and auto_pr_flag is true but gh_available is false, additionally warn: "--auto-pr was requested but gh is not installed; the orchestrator will fall back to printing compare URLs."

Step 0: Memory Retrieval (Past Issues Briefing)

Before launching any implementers, attempt to load past issue patterns from the workspace memory file. This briefing is injected into both implementer and reviewer prompts to help avoid recurring issues. The execute-plan skill shares the same memory file as the /implement skill -- patterns from both skills help each other.

Resolve the helper path

The memory helper lives in the implement skill's directory. Derive the path from the implement skill's known location in the system context (the skills list announces each skill's path). The helper is at:

memory_helper_path = dirname(<path-to-implement-SKILL.md>) + "/scripts/memory.py"

For example, if the implement skill's SKILL.md is at /root/.grok/worktrees/xai/repo/.grok/skills/implement/SKILL.md, then memory_helper_path is /root/.grok/worktrees/xai/repo/.grok/skills/implement/scripts/memory.py.

Substitute this absolute path directly into every helper invocation -- do not rely on a bash environment variable surviving across run_terminal_cmd calls. All examples below show ${MEMORY_HELPER} for readability; in practice, inline the absolute path.

Invoke the helper from the workspace root (the default cwd for run_terminal_cmd). The helper derives the workspace id from the cwd's git context.

Read Path

1. Run python3 "${MEMORY_HELPER}" snapshot via run_terminal_cmd and capture stdout. The helper prints structured JSON:

   {
     "common_issues": [
       {"category": "Error Handling", "description": "Missing null check", "count": 5}
     ],
     "recent_runs": [...],
     "exists": true
   }
   

   Store the common_issues list as existing_patterns_snapshot. Store the boolean exists as memory_existed_before.

2. If the helper exits non-zero, log a brief note, set past_issues_briefing to "", existing_patterns_snapshot to [], memory_existed_before to false, and proceed to Step 1.

3. If existing_patterns_snapshot is empty (or exists is false), set past_issues_briefing to "".

Parsing & Formatting

If existing_patterns_snapshot is non-empty:

1. Filter to only entries with count >= 2.
2. Sort by count descending.
3. Take the top 10 entries.
4. Format into past_issues_briefing:

## Past Issues to Avoid
Based on previous implementation runs, the following patterns commonly cause issues:
1. Missing null/undefined checks on function inputs (seen 5 times)
2. Missing tests for error/edge case paths (seen 8 times)

Pay special attention to these patterns in your work.

(Use time for count == 1, times otherwise.)

If there are no qualifying entries, set past_issues_briefing to "".

Graceful Degradation

If the helper command fails for any reason, set past_issues_briefing to "", existing_patterns_snapshot to [], memory_existed_before to false, and proceed normally. Never fail the run due to memory retrieval issues.

Step 1: Parse PR Plan DAG

Read the design document at <design_doc_path> using read_file.

Extract the ## PR Plan section. Parse each PR entry from ### PR N: headings into a structured representation:

PRNode {
    id: string           // e.g., "pr-1", "pr-2" -- derived from the PR number
    title: string        // PR title (text after "### PR N: ")
    slug: string         // URL-safe slug: lowercase, spaces to hyphens, non-alphanumeric removed, truncated to 50 chars
    description: string  // From the "Description:" or "**Description:**" bullet
    files: string[]      // From the "Files/components affected:" bullet
    dependencies: string[] // From the "Dependencies:" bullet, parsed as PR ids
    level: int           // Computed in Step 2
    status: string       // "pending"
    branch: string       // Computed after level assignment
    subagent_id: string  // null initially
    worktree_path: string // null initially
    base_sha: string     // null initially -- branch point before implementation
    commit_sha: string   // null initially -- HEAD after all commits (implementation + fixes)
    error: string        // null initially
    reviewer_subagent_id: string // null initially
    review_rounds: int   // 0 initially
    started_at: string   // null initially
    completed_at: string // null initially
    worktree_cleaned: bool // false initially; set true by Step 8a (per-PR prologue) or Step 9 (safety net) after `grok worktree rm --force` succeeds. Step 9 uses this to stay idempotent across resumes.
}

Parsing strategy:

1. Find the ## PR Plan section by scanning for the heading.

2. Split into individual PR entries at each ### PR heading.

3. For each entry:

   • Extract the PR number and title from the heading (e.g., ### PR 1: Add retry configuration types).

   • Extract Files/components affected: from the bullet list (split by comma).

   • Extract Dependencies: from the bullet list. Parse references like "PR 1", "PR 2" into ids like "pr-1", "pr-2". "None" means empty dependencies.

   • Extract Description: from the bullet list.

   • Generate the slug from the title:

     1. Lowercase the title.
     2. Replace spaces and underscores with hyphens.
     3. Remove any character that is not [a-z0-9-].
     4. Collapse consecutive hyphens into a single hyphen.
     5. Strip leading and trailing hyphens.
     6. Remove the suffix .lock if present (defensive -- dots are already removed in step 3, but this guards against future validation changes; git rejects refs ending in .lock).
     7. Truncate to 50 characters. If truncation lands mid-hyphen-sequence, trim trailing hyphens after truncation.
     8. If the result is empty after all transformations, use "unnamed".

     The resulting slug is safe for use in git branch names: no spaces, no .., no control characters, no ~^:?*[\, no trailing .lock, no leading/trailing dots, no consecutive dots.

   • Set id to "pr-N" where N is the PR number.

4. Validate the DAG:

   • All dependency references must resolve to valid PR ids.
   • There must be no cycles. Detect cycles by attempting topological sort -- if it fails, report the cycle and stop.
   • Every PR must have a unique id.

If parsing fails (missing PR Plan section, malformed entries, unresolved dependencies, cycles), report the error with details and stop.

Store the parsed nodes in dag.nodes.

Report to the user: "Parsed PR Plan: <N> PRs found."

Step 2: DAG Processing and Linearization

Level Assignment

Assign execution levels to each PR node:

level(node) = 0                                              if dependencies is empty
level(node) = max(level(dep) for dep in dependencies) + 1    otherwise

PRs at the same level are independent and can execute in parallel.

Linearization for Stack Assembly

Stacks (Graphite or plain-git) are strictly linear chains. The DAG is flattened into a single topologically-sorted linear sequence:

def linearize(dag):
    """Produce a linear order respecting all dependency edges."""
    nodes_by_level = group_by(dag.nodes, key=lambda n: n.level)
    result = []
    for level in sorted(nodes_by_level.keys()):
        for node in sorted(nodes_by_level[level], key=lambda n: int(n.id.split('-')[1])):
            result.append(node)
    return result

Within each level, sort by the numeric PR number (extracted from the id string via int(n.id.split('-')[1])) to produce a deterministic, reviewable order. Do NOT use lexicographic string sort on the id -- "pr-10" would sort before "pr-2" lexicographically.

Store the result in linearized_order and update the state file.

Compute Branch Names

For each PR node, compute the branch name:

branch = "execute-plan/<PLAN_ID>-<pr-number>-<slug>"

Example: execute-plan/a1b2c3d4-pr-1-add-retry-config-types

Update each node's branch field.

Report

Report to the user:

"Linearized stack order: PR1 (<title>) -> PR4 (<title>) -> PR2 (<title>) -> ...
Max parallelism: <max PRs at any single level>
Levels: <number of levels>"

Dry-Run Exit

If --dry-run was specified, report the full execution plan (linearized order, level assignments, branch names, dependency graph) and stop. Do not proceed to implementation.

Step 3: Branch Preparation

Before launching any subagents, prepare branches for all level-0 PRs (those with no dependencies). Branches for higher-level PRs are created just-in-time when their dependencies complete.

git fetch origin main

For a PR with NO dependencies (level 0):

git branch <pr.branch> origin/main
pr.base_sha = $(git rev-parse <pr.branch>)

For a PR with a SINGLE dependency (created when the dependency completes):

git branch <pr.branch> <dep.commit_sha>
pr.base_sha = $(git rev-parse <pr.branch>)

For a PR with MULTIPLE dependencies (diamond) (created when all dependencies complete):

git branch <pr.branch> <first-dep.commit_sha>

TEMP_WT=$(mktemp -d)
git worktree add "$TEMP_WT" <pr.branch>
git -C "$TEMP_WT" merge <second-dep.commit_sha> --no-edit
git worktree remove "$TEMP_WT"

pr.base_sha = $(git rev-parse <pr.branch>)

Note: Branch creation keys off the dependency's recorded commit_sha, never its branch name — this is Rule 2 of the Subagent Worktree Protocol. The main repo's refs/heads/<dep.branch> is not a reliable pointer to the dependency's latest commit; only dep.commit_sha is. The orchestrator still enforces ordering — dependent branches are created only after the dependency's process_completion step has recorded dep.commit_sha and fetched its objects.

After creating each branch, record pr.base_sha (via git rev-parse <branch_name>) and update the PR node's status to "branch_created" in the state file. The base_sha captures the exact commit the branch points to before any implementation work, and is used for range cherry-pick in Step 8a.

Critical: the orchestrator must NOT switch its own checked-out branch. Use git branch (no checkout) for branch creation and temp worktrees for merge operations.

Report to the user: "Created branches for <N> level-0 PRs. Starting implementation..."

Step 4: Execution Loop

The orchestrator uses a ready-queue approach for maximum parallelism:

ready_queue = [all PRs with status "branch_created" and all dependencies completed]
in_progress = {}
completed = {}

while ready_queue is not empty OR in_progress is not empty:
    while ready_queue is not empty AND len(in_progress) < max_concurrent:
        pr = ready_queue.pop(0)
        task_id = launch_implementer(pr)
        in_progress[pr.id] = task_id

    result = wait_commands_or_subagents(task_ids=list(in_progress.values()), mode="wait_any", timeout_ms=600000)

    for pr_id, task_id in in_progress where elapsed > PR_TIMEOUT:
        kill_command_or_subagent(task_id)
        mark pr as "failed" with error "Implementation timed out after 15 minutes"
        cascade_skip(pr_id)
        remove from in_progress

    for each completed task in result:
        finished_pr = identify_pr_from_task_id(task)
        process_completion(finished_pr, task)
        review_pr(finished_pr)

    for pr in remaining_pending:
        if all dependencies of pr are in completed:
            create_branch(pr)
            ready_queue.append(pr)

Step 4a: Launch Implementer

For each PR, launch an implementer subagent in a worktree.

After the worktree is created (by spawn_subagent's isolation: "worktree"), but before the implementer reaches git checkout, push the branch into the worktree. The branch was created in the main repo (Step 3) only after the worktree had already been built, so the worktree may not see the ref yet — this push ensures it does. Extract worktree_path from the subagent's initial output and push immediately -- the subagent's prompt processing provides a sufficient time window before git checkout is reached:

git push <worktree_path> refs/heads/<pr.branch>:refs/heads/<pr.branch>

spawn_subagent parameters:

• subagent_type: "general-purpose"
• isolation: "worktree"
• background: true
• description: "[implementer] <pr.id>: <pr.title>"

Prepend the implementer persona instructions (loaded during setup) to the prompt.

Prompt:

<implementer_persona_instructions>

---

You are implementing a single PR as part of a larger plan.

## Your PR
- Title: <pr.title>
- Description: <pr.description>
- Files to modify: <pr.files joined by comma>
- Branch: <pr.branch>

## Context from Design Document
<relevant sections from the design doc -- read and include the full design doc
content that pertains to this PR's scope>

<if past_issues_briefing is non-empty, include the following block verbatim:>
<past_issues_briefing>
Be proactive about avoiding these patterns in your implementation.
<end if>

<if user_instructions is non-empty, include the following block verbatim:>
## User Instructions
<user_instructions>
These instructions apply to all work in this plan. Follow them strictly.
<end if>

## Instructions

1. First, check out your branch:
   git checkout <pr.branch>
   This branch already contains changes from your dependencies.

2. Implement the changes described above.

3. Verify your code compiles and passes basic checks
   (e.g., cargo check, tsc --noEmit, python -m py_compile as appropriate).

4. Commit all changes with a descriptive message.
   If git commit fails with a lock error, wait 2 seconds and retry up to 3 times:
   git add -A
   git commit -m "<pr.title>

   <brief description of changes>"

5. Write an implementation summary to: ${scratch_dir}/grok-exec-summary-<PLAN_ID>-<pr.id>.md
   Include: files changed, key decisions, any deviations from the plan.

Update the PR node's status to "implementing" and started_at to the current timestamp. Persist the state file.

Report to the user: "Launching <pr.id> (<pr.title>)..."

Step 4b: Process Completion

When a subagent completes (returned by wait_commands_or_subagents):

1. Identify which PR finished by matching the returned task_id against in_progress. The wait_commands_or_subagents result contains entries with task_id, status, and output fields. Match task_id against the in_progress map to find the corresponding PR.
2. Extract subagent metadata from the result. The worktree_path and subagent_id are embedded in the spawn_subagent result's output text, wrapped in structured tags. Extract these values for state tracking.
3. Read the subagent's result:
   • If the subagent succeeded:

     • Record the subagent_id and worktree_path extracted from the result.

     • Note: pr.base_sha was already recorded in Step 3 at branch creation time. No need to compute it here.

     • Get the HEAD commit SHA:

       git -C <worktree_path> rev-parse HEAD
       

       Store as pr.commit_sha.

     • Fetch the subagent's commits into the main repo's object store, per Rule 1 of the Subagent Worktree Protocol:

       git fetch <worktree_path> HEAD --no-tags
       

       No destination refspec, no --force. Adding :refs/heads/<pr.branch> is forbidden — it can fail outright, and downstream steps key off commit_sha so the named ref never needs to be updated here.

       Then verify the SHA is reachable from the main repo so a failed fetch fails loudly here instead of much later in Step 8a (Rule 2):

       git cat-file -t <pr.commit_sha>   # must print "commit"
       

     • Update status to "reviewing".

   • If the subagent failed:
     • Record the error.
     • Update status to "failed".
     • Cascade-skip all transitive dependents (see Step 6).
     • Report: "<pr.id> (<pr.title>) FAILED: <error>"

Persist the state file after each status transition.

Report to the user on success: "<pr.id> (<pr.title>) implemented. <N> files changed. Starting review..."

Step 5: Orchestrator-Level Review

After each PR's implementation completes successfully, the orchestrator always launches a separate reviewer subagent targeting the implementer's worktree. Independent review by the reviewer persona is mandatory for every PR -- there is no self-review-only mode.

Step 5a: Launch Reviewer

Before launching the reviewer, read the PR's implementation summary at ${scratch_dir}/grok-exec-summary-<PLAN_ID>-<pr.id>.md. Based on it, identify 2-3 concrete areas the reviewer should pay extra attention to (e.g., "Verify error paths are tested", "Check that callers of renamed functions were updated"). Store as reviewer_focus_areas for this PR.

The reviewer accesses the implementer's worktree via the cwd parameter:

spawn_subagent parameters:

• subagent_type: "general-purpose"
• cwd: <pr.worktree_path>
• description: "[reviewer] <pr.id>: <pr.title>"

Prepend the reviewer persona instructions (loaded during setup) to the prompt.

Prompt:

<reviewer_persona_instructions>

---

Review the changes made for <pr.id>: <pr.title>.

The implementation summary is at: ${scratch_dir}/grok-exec-summary-<PLAN_ID>-<pr.id>.md

Review all modified files.

<if past_issues_briefing is non-empty, include the following block verbatim:>
<past_issues_briefing>
<end if>

<if user_instructions is non-empty, include the following block verbatim:>
## User Instructions
<user_instructions>
These instructions apply to all reviews in this plan. Follow them strictly.
<end if>

<if reviewer_focus_areas is non-empty:>
## Additional focus areas (from implementation summary)
<reviewer_focus_areas>
<end if>

Write review findings to:
${scratch_dir}/grok-exec-review-<PLAN_ID>-<pr.id>.md

Use the structured format:
### Issue N -- Severity: bug|suggestion|nit
- **File**: path/to/file.ext:LINE
- **Description**: <what is wrong>
- **Suggestion**: <how to fix>
- **Status**: open

If the code is clean, write a summary confirming no issues found and an empty Issues section.

Wait for the reviewer to complete. Save the returned subagent_id as pr.reviewer_subagent_id. This id is used for resume_from on subsequent review rounds (Step 5c).

Step 5b: Check Review Results

Read the review file at ${scratch_dir}/grok-exec-review-<PLAN_ID>-<pr.id>.md. Count issues with Status: open.

For each open issue found, extract a concise one-line description and append it to issue_patterns (skip exact duplicates already in the list). These are accumulated across all PRs and all review rounds for the entire run, and used in Step 10 (Memory Flush).

Count open issues by severity (bug, suggestion, nit) and add the counts to total_issues_by_severity.

Increment pr.review_rounds (this counts total reviews performed, including the initial one).

If 0 open issues:

• The PR is done. Update status to "completed", set completed_at.
• Persist the state file.
• Report: "<pr.id> review: 0 issues found. PR complete."
• Return to the execution loop (Step 4).

If any open issues:

• Enter a review-fix loop. Resume the implementer to fix (Step 5c), then resume the reviewer to re-review. Repeat until 0 open issues.
• There is no iteration cap. Every issue -- including nits and suggestions -- must be addressed before the PR is marked completed.
• See Step 5c.

Report: "<pr.id> review round <review_rounds>: <N> issues found (<X> bugs, <Y> suggestions, <Z> nits). Fixing..."

Step 5c: Fix Cycle

Resume the original implementer to fix all review issues:

spawn_subagent parameters:

• subagent_type: "general-purpose"
• resume_from: <pr.subagent_id>
• description: "[implementer] Fix review issues for <pr.id>"

Prompt:

The reviewer found issues. The review file is at:
${scratch_dir}/grok-exec-review-<PLAN_ID>-<pr.id>.md

Read the review file. Address ALL issues with Status: open -- including nits,
suggestions, and any style or hint-level feedback. Nothing is too small to fix.

For each issue, implement the fix, then update the review file:
- Change Status: open -> Status: fixed
- Add a Response field explaining what you changed

You are encouraged to push back on feedback that doesn't make sense, is
contradictory, or would make the implementation worse. If you disagree with
an issue:
- Set Status: wontfix
- Write a clear, technical explanation of why the reviewer's suggestion is
  wrong or counterproductive
- Do NOT comply with feedback just to make a reviewer happy -- defend good
  implementation decisions

Commit all fixes:
git add -A
git commit -m "fix: address review feedback for <pr.title>"

<if user_instructions is non-empty, include the following block verbatim:>
## User Instructions
<user_instructions>
These instructions apply to all work in this plan. Follow them strictly.
<end if>

Wait for the implementer to complete. Update pr.subagent_id with the new returned id. Read the review file to note any issues the implementer marked Status: wontfix (needed for stalemate detection below).

After the fix, re-fetch the subagent's new commits using the same form as Step 4b (Rule 1 of the Subagent Worktree Protocol):

git fetch <worktree_path> HEAD --no-tags

Then update the commit SHA:

pr.commit_sha = $(git -C <worktree_path> rev-parse HEAD)
git cat-file -t <pr.commit_sha>   # must print "commit"

No destination refspec, no --force — both are unnecessary because commit_sha is what downstream steps use, and the subagent is the sole writer for this branch so the fetch is always a simple object pull.

Resume the reviewer to re-review.

spawn_subagent parameters:

• subagent_type: "general-purpose"
• resume_from: <pr.reviewer_subagent_id>
• description: "[reviewer] Re-review <pr.id>: <pr.title> (round <review_rounds>)"

Prompt:

The implementer has addressed the feedback. Re-review the changes.

Review file location: ${scratch_dir}/grok-exec-review-<PLAN_ID>-<pr.id>.md

Re-read the review file and all modified files. For each existing issue:
- If fixed properly: leave Status: fixed
- If not fixed or fix introduced new problems: set Status: open with updated description

Check for regressions introduced by the fixes.

Append any NEW issues found using the structured format:
### Issue N -- Severity: bug|suggestion|nit
- **File**: path/to/file.ext:LINE
- **Description**: <what is wrong>
- **Suggestion**: <how to fix>
- **Status**: open

Accept convincing wontfix justifications -- do not reopen issues where the
implementer provided a sound technical rationale.

<if past_issues_briefing has accumulated new patterns since the previous review round, include the updated block verbatim:>
<past_issues_briefing>
<end if>

<if user_instructions is non-empty, include the following block verbatim:>
## User Instructions
<user_instructions>
These instructions apply to all reviews in this plan. Follow them strictly.
<end if>

Wait for completion and update pr.reviewer_subagent_id with the new returned id.

Fallback on resume failure: If resume_from fails (e.g., subagent expired, quota exceeded, or internal error), fall back to launching a fresh reviewer with cwd: <pr.worktree_path> using the same prompt template as Step 5a (including reviewer persona instructions, past_issues_briefing, reviewer_focus_areas, and user_instructions). Update pr.reviewer_subagent_id with the new task id. This ensures the review-fix loop is never blocked by a stale or expired subagent reference.

This is the next review round. Read the new review results. For each open issue found, extract a one-line description and append to issue_patterns (skip exact duplicates). Count open issues by severity and add to total_issues_by_severity. Increment pr.review_rounds.

• If 0 issues: mark "completed".
• If issues remain: repeat the fix cycle (fix, then resume the reviewer).
• There is no iteration cap.
• Stalemate detection: If the implementer sets Status: wontfix on an issue and the next reviewer re-opens the same issue (matched by file reference and description), the implementer and reviewer have reached a disagreement. Escalate to the user: frame the dispute clearly, present both positions, and let the user decide. The user's decision is final -- resume the implementer with the decision and set the issue to Status: fixed.

Report: "<pr.id> fix cycle complete. Re-reviewing (round <review_rounds>)..."

Persist the state file. Return to the execution loop (Step 4).

Step 6: Failure Handling

When a PR fails (implementation error, unfixable review issues, or branch creation failure):

Cascade-Skip

Mark the failed PR as "failed" with the error details. Then cascade-skip all transitive dependents:

def cascade_skip(failed_pr_id, all_prs):
    for pr in all_prs:
        if pr.status == "pending" or pr.status == "branch_created":
            if failed_pr_id in transitive_dependencies(pr):
                pr.status = "skipped"
                pr.error = "Skipped: dependency <failed_pr_id> failed"

Remove any skipped PRs from the ready_queue. Do not abort the entire run -- independent PRs continue executing.

Report:

"<pr.id> (<pr.title>) FAILED: <error>
Dependent PRs skipped: <list of skipped pr ids and titles>
Independent PRs continue running."

Persist the state file after all status updates.

Step 7: Resumption

When invoked with --resume <PLAN_ID>:

Setup is skipped on resume, so first recompute the scratch directory — the state file and all per-PR artifacts live under it. This assumes the same $TMPDIR as the original run:

scratch_dir="${TMPDIR:-/tmp}/grok-$(id -u)"; mkdir -p "$scratch_dir" && chmod 700 "$scratch_dir" && echo "$scratch_dir"

1. Read the state file at ${scratch_dir}/grok-exec-plan-<PLAN_ID>.json.
2. If the file does not exist, report the error and stop.
3. Restore orchestrator state from the file: design_doc_path, effort, max_concurrent, dag, linearized_order, user_instructions, no_graphite_flag, auto_pr_flag, graphite_available, gh_available, pr_urls, pr_create_commands. Apply these defaults for any field missing from a pre-existing (pre-this-feature) state file:
   • no_graphite_flag: false
   • auto_pr_flag: false
   • pr_create_commands: []
   • graphite_available and gh_available: re-run the Step 0.5 probe (both gt and gh) to populate them.
4. Evaluate each PR node's status:
   • completed: Skip. The commit SHA is already recorded.
   • failed: Clean up the old worktree first (if worktree_path is set and worktree_cleaned is false, run grok worktree rm --force <worktree_path>), then reset to "pending". Clear error, subagent_id, reviewer_subagent_id, worktree_path, base_sha, commit_sha, review_rounds, worktree_cleaned. This PR will be retried from scratch with a new worktree.
   • skipped: Re-evaluate. If all dependencies are now "completed", reset to "pending". Otherwise, keep as "skipped".
   • implementing or reviewing: The previous run crashed mid-execution. Clean up the old worktree first (if worktree_path is set and worktree_cleaned is false, run grok worktree rm --force <worktree_path>), then reset to "pending" for a clean retry. Clear subagent_id, reviewer_subagent_id, worktree_path, base_sha, commit_sha, review_rounds, worktree_cleaned.
   • pending or branch_created: Keep as-is.
5. If stack_assembly_started is true but graphite_stack_submitted is false (recall: in plain-git mode this flag means "Step 8b finished" — so the gate fires for both modes):
   • The previous run crashed during stack assembly.
   • Graphite mode (graphite_available == true): clean up partial Graphite state — check for branches tracked by Graphite with gt ls, delete any partial branches with gt delete, reset to main.
   • Plain-git mode (graphite_available == false): bring the orchestrator's workspace back to a known baseline before deleting any branches. The resumption path must tolerate arbitrary in-flight state from the prior crash — the two realistic mid-Step-8a crash sites are (a) after git checkout -B "<pr.branch>" with HEAD on a doomed branch, and (b) mid-cherry-pick with unstaged conflict markers in the working tree (in which case a plain git checkout main would refuse with "Your local changes to the following files would be overwritten by checkout."). Cleanup sequence handles both:

     git cherry-pick --abort 2>/dev/null || true
     git merge --abort 2>/dev/null || true
     git rebase --abort 2>/dev/null || true
     
     git fetch origin main
     git checkout -f main
     git reset --hard origin/main
     
     while IFS= read -r branch; do
       git branch -D "$branch"
     done < <(git for-each-ref --format='%(refname:short)' "refs/heads/execute-plan/<PLAN_ID>-*")
     

   • Set stack_assembly_started to false and clear stack_assembly_progress.
6. Re-read the design document to restore full context.
7. Resume execution from Step 3 (branch preparation for any PRs that need branches) and Step 4 (execution loop).

Report: "Resuming PLAN_ID <PLAN_ID>. <N> completed, <M> to retry, <K> skipped."

Step 8: Stack Assembly

After all PRs in the linearized order are either "completed" or "failed"/"skipped", and at least one PR completed successfully, assemble the stack. The exact mechanism branches on graphite_available:

• If graphite_available == true -> use Step 8a (Graphite mode) below.
• If graphite_available == false -> skip Step 8a and use Step 8a (plain-git mode) instead.

Step 8b (PR URL collection) and Step 8c (reporting) likewise branch.

Update stack_assembly_started to true in the state file before beginning.

Step 8a (Graphite mode): Build the Stack

Work in the main workspace. The stack is built in the linearized topological order, skipping any failed/skipped PRs.

Per-PR prologue — free the branch name. Apply Rule 3 of the Subagent Worktree Protocol before touching the PR's branch ref: tear down the subagent worktree so gt create can move/recreate refs/heads/<pr.branch> cleanly. Run the cleanup unconditionally — it is a no-op when the worktree is already gone or never existed (e.g., a failed/skipped PR was never assigned one, or a --resume of a partial Step 8a has already cleaned it):

if [ -n "<pr.worktree_path>" ] && [ -d "<pr.worktree_path>" ]; then
  grok worktree rm --force "<pr.worktree_path>"
fi

After cleanup, perform the per-PR stack step:

git checkout main
git pull origin main

gt create "<pr.branch>" --no-interactive

git cat-file -t <commit_sha>

git cherry-pick <base_sha>..<commit_sha> --allow-empty


gt submit --stack --no-edit --no-interactive

(git checkout main and git pull origin main are the one-time prologue at the very top of the loop, not per-PR. gt submit --stack is the one-time epilogue after all PRs have been added with gt create.)

Update graphite_stack_submitted to true in the state file. After the per-PR cleanup runs successfully, set pr.worktree_cleaned = true in the state file so Step 9 knows to skip this worktree.

Cherry-pick conflict handling:

• Cherry-pick conflicts should be rare because dependent PRs were implemented on branches containing their dependencies' changes.
• If a conflict occurs, the orchestrator resolves it directly — do not stop or ask the user:
  1. Identify the conflicting files from the cherry-pick output.
  2. Read each conflicting file in full using read_file. During cherry-pick, HEAD (top section) is the current stack tip (Graphite branch in Graphite mode, plain-git branch otherwise); the bottom section is the PR's incoming changes.
  3. Resolve by combining both sides' intent: keep non-overlapping additions in logical order, merge overlapping edits preserving the PR's intended new behavior.
  4. Remove all conflict markers (<<<<<<<, =======, >>>>>>>).
  5. Write resolved content using the write tool.
  6. Stage resolved files: git add <resolved_files>
  7. Continue the cherry-pick: git cherry-pick --continue
  8. After resolving, verify the result compiles (scope to affected targets, e.g. bazel build //pkg:target). If verification fails, attempt to fix the resolution; if still failing, treat as unresolvable (step 9).
  9. If the conflict is truly unresolvable (fundamentally incompatible changes), abort (git cherry-pick --abort), mark the PR as "failed" with conflict details, cascade-skip dependents, and continue assembling the remaining stack.

Why range cherry-pick (base_sha..commit_sha): Each PR may have multiple commits (initial implementation + fix commits from review cycles). The range cherry-pick replays all of them in order. base_sha is the branch point recorded in Step 3 at branch creation time (before any implementation commits). commit_sha is the final HEAD after all fix cycles. This ensures the diff shows exactly all changes that PR introduced -- not accumulated dependency changes, and not just the last fix commit.

Step 8a (plain-git mode): Build the Stack

When graphite_available == false, assemble the same linearized stack using only plain git. Each PR becomes its own branch fast-forwarded from the previous PR's branch (or from main for the bottom of the stack).

Work in the main workspace. Skip any failed/skipped PRs. Track the previous successfully-pushed branch in a local variable parent_branch (initialized to "main").

Important Step 3 ↔ Step 8a interaction: Step 3 already created each <pr.branch> in the main repo (via git branch <pr.branch> <base>). Step 4b deliberately does not advance that ref — it only pulls the subagent's objects into the main repo's store and records pr.commit_sha (Rule 2 of the Subagent Worktree Protocol). So by the time Step 8a runs, every <pr.branch> already exists locally and its tip is not guaranteed to be commit_sha. Step 8a needs to reset each branch to a new starting point (parent_branch from this stack-assembly pass), not create it from scratch — hence git checkout -B (uppercase) below. The per-PR grok worktree rm --force immediately above the checkout -B is required by Rule 3 — without it the reset can fail with cannot force update the branch '...' used by worktree at '<WT>'.

test -z "$(git status --porcelain)" || { echo "Working tree dirty; aborting"; exit 1; }
git fetch origin main
git checkout main
git reset --hard origin/main
parent_branch="main"

Then, per PR (in linearized stack order):

# Free the branch name (Rule 3 of the Subagent Worktree Protocol).
# Idempotent — no-op when the WT is already gone, missing, or was never
# assigned (e.g., a failed/skipped PR). Without this, `git checkout -B
# "<pr.branch>"` can fail with
# `cannot force update the branch '<pr.branch>' used by worktree at '<WT>'`.
if [ -n "<pr.worktree_path>" ] && [ -d "<pr.worktree_path>" ]; then
  grok worktree rm --force "<pr.worktree_path>"
fi

git checkout -B "<pr.branch>" "$parent_branch"

git cat-file -t <commit_sha>

git cherry-pick <base_sha>..<commit_sha> --allow-empty

git push --force-with-lease origin "<pr.branch>"

parent_branch="<pr.branch>"

After the cleanup runs successfully, set pr.worktree_cleaned = true in the state file so Step 9 knows to skip this worktree.

Cherry-pick conflict handling for resolvable conflicts is identical to Graphite mode (see the Cherry-pick conflict handling block above). The resolution protocol — read each conflicting file, combine intents, remove markers, write resolved content, git add, git cherry-pick --continue, verify compile — applies unchanged.

For unresolvable conflicts, plain-git mode adds an explicit cleanup step before continuing the loop (the Graphite-mode block leaves cleanup to gt internals; plain-git needs to do it manually so the orchestrator is in a known state):

git cherry-pick --abort
git checkout main

Then mark the PR "failed", cascade-skip its dependents, and do not advance parent_branch — the next non-skipped PR's branch is created off parent_branch, which still points at the last successfully-pushed branch (or main if nothing has been pushed yet).

Push failure handling: If git push --force-with-lease itself fails (network blip, permission revoked, stale lease, etc.), retry once after a 5-second pause. If the retry also fails, mark the PR "failed" with the push error, cascade-skip dependents, and do not advance parent_branch. The next non-skipped PR continues from the last successfully-pushed branch — the half-pushed stack is recorded in stack_assembly_progress, so a --resume invocation can rebuild from the last good point.

No equivalent of gt submit: PRs are not auto-created by default. After the loop completes, jump to Step 8b (plain-git mode) for URL collection / optional --auto-pr.

Update stack_assembly_started to true (already done) but do not set graphite_stack_submitted in this mode yet -- in Graphite mode that flag literally means "gt submit succeeded"; in plain-git mode it is reused as a generic "Step 8b finished" sentinel. After Step 8b completes successfully (whether --auto-pr ran or not), Step 8b sets graphite_stack_submitted = true so Step 7 resumption logic treats the run as assembly-complete.

Step 8b (Graphite mode): Collect PR URLs

After gt submit succeeds, collect the PR URLs:

gt ls --json

Parse the output to extract PR URLs for each branch. Store in pr_urls in the state file.

Report: "Stack submitted: <N> PRs. URLs: [...]"

Step 8b (plain-git mode): Collect PR URLs

After all branches are pushed, derive a GitHub-style compare URL for each branch in stack order. The parsing supports both github.com and GitHub Enterprise (github.<host>) remotes.

remote_url=$(git config --get remote.origin.url)

Parse remote_url into (host, owner, repo). Accept any of these forms, in order:

1. git@<host>:<owner>/<repo>[.git] (canonical SSH)
2. ssh://git@<host>[:port]/<owner>/<repo>[.git] (scheme-prefixed SSH)
3. https://[<user>[:<pass>]@]<host>/<owner>/<repo>[.git][/] (HTTPS, optionally with embedded credentials and/or trailing slash)

A pragmatic regex that captures all three (operate against the trimmed remote URL):

^(?:git@|ssh://(?:[^@]+@)?|https?://(?:[^@/]+@)?)([^:/]+)[:/](?:[^/]+/)*([^/]+)/([^/]+?)(?:\.git)?/?$

Capture groups: host, owner, repo. Strip any user[:pass]@ segment before logging the URL anywhere to avoid leaking credentials embedded in the remote URL.

• If host does not match github.com or github.* (e.g., github.example.com for GHE), or if the regex fails entirely, the remote is non-GitHub. Skip compare-URL synthesis and skip gh pr create (even if --auto-pr was set). Instead, populate pr_urls with {branch: <pr.branch>, url: null, kind: "pushed-only", note: "non-GitHub remote (<remote_url with credentials stripped>) — open a PR via your forge UI"} for each pushed branch so the Final Report still tells the user what was pushed and where. Continue to the final report.

Otherwise, for each PR in linearized stack order, compute:

compare_url = "https://<host>/<owner>/<repo>/compare/<parent_branch>...<pr.branch>?expand=1"

where <parent_branch> is the branch immediately below this PR in the stack (or main for the bottom).

pr_urls in plain-git mode is a list of objects, one per pushed branch in stack order. The exact shape per entry is:

{
  "branch": "<pr.branch>",
  "url": "<URL string or null>",
  "kind": "pr"     // a real PR opened via gh pr create
              | "compare" // a GitHub compare URL the user must open manually
              | "pushed-only", // non-GitHub remote; branch is pushed but no URL synthesizable
  "note": "<optional explanatory string, e.g., for pushed-only entries>"
}

The note field is optional: it is populated for pushed-only entries (to explain why no URL is available — see the non-GitHub-remote branch above) and may also be attached to compare entries that resulted from a failed gh pr create invocation (to record the original error). The Final Report renders note verbatim when present.

If auto_pr_flag == true AND gh_available == true AND host is GitHub/GHE: create draft PRs by invoking gh in stack order:

gh pr create --base "<parent_branch>" --head "<pr.branch>" --fill --draft

Capture stdout (the URL of the created PR) and append an entry with kind: "pr" and the captured URL. If gh pr create fails for a single branch (rate limit, validation error, etc.), log the failure with the branch name, append an entry with kind: "compare" and the synthesized compare URL instead, and continue with the next PR. The downstream PR's --base still points at the failed PR's branch (not a PR) — that's correct, since the branch was pushed; the user just needs to also open a PR for the failed branch via the compare URL. Sequential — never parallel — to preserve ordering.

Otherwise (no --auto-pr, or no gh): populate every entry with kind: "compare" and the synthesized compare URL. Also build a list of suggested copy/paste commands:

gh pr create --base <parent_branch> --head <pr.branch> --fill --draft

one per PR in stack order. Store this list as pr_create_commands in the state file for the final report.

Persist the state file. Set graphite_stack_submitted = true (generic "Step 8b finished" sentinel — see the Setup notes on the dual semantics).

Report (the variant depends on the mix of entry kinds):

• All kind: "pr": "Stack pushed and PRs created: <N> branches. URLs: [...]"
• All kind: "compare": "Stack pushed: <N> branches. Open these compare URLs (or run the gh pr create commands) to open PRs: [...]"
• Mixed kind: "pr" and kind: "compare" (some gh pr create calls failed during --auto-pr): "Stack pushed: <N> branches. <X> PRs were created via gh, <Y> need to be opened manually via the printed compare URLs."
• Any kind: "pushed-only" (non-GitHub remote): "Stack pushed: <N> branches to non-GitHub remote. Open PRs via your forge UI."

Step 9: Cleanup

After successful stack assembly:

for each pr in dag.nodes:
    if pr.subagent_id is not null:
        kill_command_or_subagent(pr.subagent_id)
    if pr.reviewer_subagent_id is not null:
        kill_command_or_subagent(pr.reviewer_subagent_id)

# PR worktrees are normally cleaned during Step 8a (per-PR prologue) so the
# stack branches can be safely manipulated. This loop is the safety net for
# any worktree that escaped Step 8a — e.g., the WT belonged to a `failed` or
# `skipped` PR (Step 8a never reaches them) or Step 8a crashed before
# reaching this PR. The check on `worktree_cleaned` keeps Step 9 idempotent
# on `--resume`.
for each pr in dag.nodes where worktree_path is not null
                          and not pr.worktree_cleaned:
    if directory <worktree_path> exists:
        grok worktree rm --force <worktree_path>
    pr.worktree_cleaned = true

rm -f ${scratch_dir}/grok-exec-summary-<PLAN_ID>-*.md
rm -f ${scratch_dir}/grok-exec-review-<PLAN_ID>-*.md

Keep the state file -- the user may want to reference PR URLs or run history. It can be manually removed:

rm ${scratch_dir}/grok-exec-plan-<PLAN_ID>.json

After failure (resumable): Worktrees for completed PRs are preserved (their commits are needed for stack assembly). Worktrees for failed or crashed PRs are cleaned up during --resume (Step 7) before retrying, since failed PRs are retried from scratch with new worktrees.

Note: grok worktree rm --force is used instead of git worktree remove to avoid inconsistencies with the tool's internal worktree tracking (same pattern as pr-babysit skill).

Step 10: Memory Flush

After cleanup, update the workspace memory file with patterns from this run. The orchestrator performs this directly using its own tools -- no subagent is needed. This step follows the same protocol as the /implement skill's Step 6 (see .grok/skills/implement/SKILL.md for full helper documentation, exit codes, and file format details).

Step 10a: Collect & Categorize This Run's Patterns

1. Use the issue_patterns list accumulated during Step 5b and Step 5c re-reviews across all PRs and review rounds.
2. Generalize each pattern. The memory file exists to help future runs on different tasks — patterns that reference this task's specific code, variable names, or domain objects are useless noise. Strip implementation-specific details (file names, variable names, type names, function names, domain-specific terms) and rewrite each pattern as a reusable principle that applies across different codebases and tasks:
   • Bad: "Missing error type RetryableError in retry handler list" → Good: "Missing entries in error-type or configuration allowlists"
   • Bad: "JWT token not validated for expiration" → Good: "Missing expiration/TTL validation on tokens or credentials"
   • Bad: "calculateTotal function exceeds 80 lines" → Good: "Functions exceeding reasonable length without decomposition"
   • Bad: "No test for handleUserAuth error path" → Good: "Missing tests for error/edge case paths"
   • Bad: "Missing null check on userId parameter" → Good: "Missing null/undefined checks on function inputs" If a pattern is already general (e.g., "Missing null checks on function inputs"), keep it as-is. If multiple task-specific patterns generalize to the same reusable principle, collapse them into one entry.
3. Categorize each generalized pattern into one of: Error Handling, Testing, Security, Code Quality, Naming, Documentation, Performance, or another short category name. Reuse existing category names from existing_patterns_snapshot (captured in Step 0) whenever the pattern fits.
4. For each pattern, write a concise one-line description. Keep descriptions on a single line.

Step 10b: Harmonize Phrasing Against Existing Entries

Before handing generalized patterns to the helper, dedup at the phrasing level using existing_patterns_snapshot:

1. For each of this run's patterns, scan existing_patterns_snapshot for a semantically equivalent entry. If a match exists, replace this run's description with the exact existing description string.
2. If no match exists, keep the concise description as-is.
3. Within this run's own list, also dedup by phrasing -- collapse patterns that mean the same thing to a single entry.

Step 10c: Build the Update Spec

Construct a JSON object:

{
  "patterns": [
    {"category": "Error Handling", "description": "Missing null/undefined checks on function inputs"},
    {"category": "Testing", "description": "Missing tests for error/edge case paths"}
  ],
  "run": {
    "date": null,
    "description": "Execute plan: <design doc title or short description>",
    "rounds": <sum of review_rounds across all completed PRs>,
    "issues_by_severity": {"bug": <total>, "suggestion": <total>, "nit": <total>},
    "key_patterns": ["<2-3 most significant patterns from this run>"],
    "specializations": ["general"]
  }
}

Field notes:

• run.date: pass null and the helper fills in today's UTC date.
• run.rounds: sum of review_rounds across all completed PRs.
• run.issues_by_severity: derived from total_issues_by_severity (accumulated in Step 5b and Step 5c re-reviews across all PRs).
• run.key_patterns: pick 2-3 most-significant patterns (severity-ranked: bugs > suggestions > nits). Apply the same generalization rules as Step 10a — strip task-specific names and rewrite as reusable principles.
• run.specializations: always ["general"] for execute-plan (only the reviewer persona is used).

Step 10d: Invoke the Helper

Use the write tool to create ${scratch_dir}/grok-exec-mem-${PLAN_ID}.json with the JSON spec above, then invoke:

python3 "${MEMORY_HELPER}" update < ${scratch_dir}/grok-exec-mem-${PLAN_ID}.json

The helper acquires the lock, merges, compacts, writes atomically, and prints a JSON stats summary on stdout:

{
  "file": "/path/to/implement-memory/<workspace-id>.md",
  "existed_before": true,
  "stats": {
    "new_patterns": 2,
    "merged_patterns": 5,
    "categories_touched": ["Error Handling", "Testing"],
    "categories_capped": {},
    "recent_runs_dropped": 0
  }
}

Use these stats to report to the user:

"Memory updated: 2 new patterns, 5 merged into existing entries."

Or if existed_before is false:

"Memory file created with N patterns."

Graceful Degradation

If the helper exits non-zero, log a warning with stderr and skip the memory update. The implementation is already complete and reviewed -- never fail the run due to memory flush issues. Clean up the temp JSON file regardless:

rm -f ${scratch_dir}/grok-exec-mem-${PLAN_ID}.json

Final Report

After stack assembly, cleanup, and memory flush, present a final report:

1. Summary -- which PRs were implemented, total files changed across all PRs.
2. Execution stats:
   • Total PRs: N (M completed, K failed, J skipped)
   • Levels: L, Max parallelism achieved: P
   • Effort level: E
3. Review stats -- total review rounds across all PRs, total issues found and fixed.
4. Stack -- linearized order, branch names, and URLs.
   • Graphite mode: label this section "Graphite stack" and list the PR URLs from gt ls --json.
   • Plain-git mode: label this section "Git branch stack" and render pr_urls entries by kind. If a note field is present on the entry, append it verbatim to the rendered line (in parentheses or on a continuation line).
     • kind: "pr": print as "PR: <url>" (plus note if present — no current code path attaches one, but the renderer accepts a note field on this kind to keep the rendering rules uniform across all three kinds).
     • kind: "compare": print as "Compare URL: <url> — open this to create the PR", append the matching command from pr_create_commands, and append note if present.
     • kind: "pushed-only": print as "Pushed: <branch> — <note>" (the note is always present for this kind; it carries the user-facing explanation, e.g., "non-GitHub remote (<remote_url>) — open a PR via your forge UI").
5. Failed PRs (if any) -- which PRs failed and why, which were skipped as a result.
6. Resumption -- if any PRs failed: "Resume with: /execute-plan --resume <PLAN_ID>"
7. Memory update -- what patterns were written or updated in the workspace memory file. Use the existed_before flag from the helper's Step 10d update output to choose between "file created" and "file updated" wording.
8. Next steps:
   • Graphite mode: suggest /pr-babysit add <bottom-pr-number> to monitor CI and reviews.
   • Plain-git mode: do NOT suggest /pr-babysit (it depends on gt for stack walking — see its Step 2/3). The Stack section above already lists the URLs / commands; the Next-Steps text just adds a one-line note: "No automated CI/review monitoring is available in plain-git mode; open the PR URLs / compare URLs above and monitor them in the GitHub UI."

In-Progress Reporting

Give the user a brief status update after each significant event:

• After parse: "Parsed PR Plan: <N> PRs, <L> levels, max parallelism: <P>"
• After linearize: "Linearized stack order: PR1 -> PR4 -> PR2 -> PR5 -> PR3"
• After branch creation: "Created branches for <N> level-0 PRs. Starting implementation..."
• After launching a PR: "Launching <pr.id> (<pr.title>)..."
• After PR implementation completes: "<pr.id> (<pr.title>) implemented in <duration>. <N> files changed. Starting review..."
• After review (0 issues): "<pr.id> review: 0 issues found. PR complete."
• After review (N issues): "<pr.id> review: <N> issues (<X> bugs, <Y> suggestions, <Z> nits). Fixing..."
• After fix cycle: "<pr.id> fix applied. Re-reviewing (round <N>)..."
• After PR fully complete: "<pr.id> complete. <M> of <total> PRs done. <K> newly ready."
• After failure: "<pr.id> FAILED: <reason>. Skipping <N> dependents. <M> independent PRs continue."
• After all PRs done: "All PRs complete. Building <Graphite|git branch> stack..." (pick the label based on graphite_available)
• After stack submission (Graphite mode): "Stack submitted: <N> PRs. URLs: [...]"
• After stack push (plain-git mode, no --auto-pr): "Stack pushed: <N> branches. Open these compare URLs (or run the gh pr create commands) to open PRs: [...]"
• After stack push (plain-git mode, with --auto-pr, all succeeded): "Stack pushed and draft PRs created: <N> branches. URLs: [...]"
• After stack push (plain-git mode, with --auto-pr, mixed results): "Stack pushed: <N> branches. <X> PRs created via gh, <Y> need manual creation via the printed compare URLs."
• After stack push (plain-git mode, non-GitHub remote): "Stack pushed: <N> branches to non-GitHub remote. Open PRs via your forge UI."
• After cleanup: "Cleanup complete."
• After memory flush: "Memory updated with N patterns from this run." (or "Memory file created with N patterns." for first run)
• After final report (Graphite mode only): "Run '/pr-babysit add <bottom-pr-number>' to monitor CI."

Safety Guardrails

Follow these rules strictly:

• Never force-push without --force-with-lease. Always use git push --force-with-lease, never git push --force. gt submit handles this internally. In plain-git mode the orchestrator uses git push --force-with-lease origin <branch> unconditionally — the lease is a no-op for newly-created branches (no upstream to lease against), but protects the resume case, the rare concurrent-push case, and the re-resolved-conflict case.

• Never modify the main branch. The orchestrator checks out main only during stack assembly (to cherry-pick onto stack branches). Never commit directly to main.

• Orchestrator owns all git/stack-tooling operations, including merge conflict resolution. Subagents implement code and commit in worktrees. They never create branches, push, or interact with Graphite or gh. The orchestrator resolves merge conflicts directly during branch preparation (Step 3) and stack assembly (Step 8a) using read_file and write — this is the sole exception to the "no source file modification" rule.

• Sequential stack assembly operations. All branch-mutating and remote-mutating operations during Step 8 (Graphite: gt create, gt submit; plain-git: git checkout -B, git cherry-pick, git push --force-with-lease origin, gh pr create) run sequentially. Never run them concurrently — ordering is load-bearing for stack consistency.

• Follow the Subagent Worktree Protocol exactly. It is the only contract for moving commits and refs between a subagent's worktree and the orchestrator's main repo:

  • Step 4b/5c fetch with git fetch <WT> HEAD --no-tags — no destination refspec, no --force.
  • Step 3, 4b, 5c, 8a all treat pr.commit_sha (not refs/heads/<pr.branch>) as the authoritative reference for a PR's changes.
  • Step 8a tears down each PR's subagent worktree with grok worktree rm --force immediately before manipulating that PR's branch ref.

  See the Subagent Worktree Protocol section near the top of this document for the full rules. There is no git lock contention between worktrees. Subagent prompts instruct retry on git lock errors as a general safety measure, but contention is not expected.

• All fix work happens in worktrees, never in the main workspace. The orchestrator's workspace tree must not be modified by subagents.

• Use grok worktree rm --force for subagent worktrees (created by isolation: "worktree"). This avoids inconsistencies with the tool's internal worktree tracking. Use git worktree remove for temporary merge worktrees created directly by the orchestrator in Step 3 (diamond dependency handling) -- these are not tracked by the tool's internal registry.

• Persist state after every status transition. If the session crashes, the state file enables resumption.

• Never merge PRs. The skill creates and submits PRs. Merging is a human decision.

• Explicit composition with /pr-babysit (Graphite mode only). After stack submission, the user runs /pr-babysit add <bottom-pr-number> separately. The skill does not auto-chain. In plain-git mode, /pr-babysit is not suggested because it depends on gt for stack walking (it invokes gt checkout, gt bottom, gt up, gt sync).

Rules

• Inject personas into prompts -- always prepend the implementer or reviewer persona instructions (from the shared personas file) to the subagent prompt on initial launches. Do NOT pass a persona parameter to spawn_subagent. On resume_from follow-ups, the persona is already in the subagent's transcript from the initial launch.
• Prefix description with a bracketed role tag -- [implementer] for implementer launches and fix cycles, [reviewer] for reviewer launches and re-reviews. The pager parses the first [tag] of the description and uses it as the row label (the bracketed prefix is stripped from the displayed description). Without this, every row falls through to the generic "General" label because subagent_type is general-purpose and no persona/role is plumbed through the spawn args. Keep the tag on resume_from follow-ups so the label stays stable across rounds.
• isolation: "worktree" for implementers only -- implementers get fresh worktrees. Reviewers use cwd=<worktree_path> to access an existing worktree.
• Include design context in initial prompts -- the initial implementer and initial reviewer launches should include all relevant design context in their task prompts. All subsequent rounds use resume_from instead, which carries the subagent's own transcript forward.
• resume_from for fix and re-review cycles -- when resuming an implementer to fix review issues, use resume_from with the stored subagent_id (implementer -> implementer). When resuming a reviewer for subsequent review rounds, use resume_from with the stored reviewer_subagent_id (reviewer -> reviewer). Both are same-persona resumptions.
• background: true for parallel launches -- implementation subagents are launched in background. Use wait_commands_or_subagents(task_ids=[...], mode="wait_any") for event-driven waiting.
• Save every subagent_id returned by spawn_subagent -- needed for resume_from on both implementer fix cycles and reviewer re-review rounds. Update pr.subagent_id after each implementer task and pr.reviewer_subagent_id after each reviewer task.
• Read review files yourself after each review to count open issues and decide whether to continue.
• Do not modify the implementation yourself -- all code changes go through the implementer persona subagent.
• Explicitly tell subagents to write their output files -- include file paths and expected content in every prompt.
• Thread the same file paths across all rounds per PR -- never generate new paths between iterations.
• Include the design doc context in subagent prompts -- read the design document and include the relevant sections for each PR in the implementer prompt.
• Branch creation is just-in-time -- create branches for dependent PRs only after their dependencies complete. Level-0 branches are created upfront.
• State file is the source of truth -- persist after every status transition. On resume, the state file determines what to retry.
• Cascade-skip, do not abort -- a failed PR causes its transitive dependents to be skipped, but independent PRs continue.
• Error handling -- if a subagent fails or cannot be resumed, mark the PR as failed, cascade-skip dependents, and continue with independent PRs. Only stop the entire run if no PRs can make progress.
• Context management for resumed subagents -- resume_from carries the full prior transcript. If a review-fix loop exceeds 4 rounds, consider killing the reviewer task and launching a fresh reviewer (with cwd) to prevent token overflow. Reset pr.reviewer_subagent_id to the new task id. The same applies to implementers if fix cycles are unusually long.
• Stack assembly is batch, not incremental -- wait for all PRs to complete (or fail/skip) before assembling the stack. Do not assemble incrementally.
• Respect concurrency limits -- never launch more than max_concurrent subagents simultaneously. The ready-queue loop enforces this.
• past_issues_briefing must be consistent and capped -- before launching any implementer or reviewer, the orchestrator must build the past_issues_briefing from the issue_patterns list accumulated so far. If the list exceeds 20 patterns, include only the top 20 by occurrence count (most frequently seen patterns first). Never partially include a pattern or truncate mid-description. If issue_patterns is empty (first PR, no prior reviews), omit the block entirely rather than including an empty block.
• Memory is best-effort -- if the memory.py helper fails (lock contention, malformed spec, disk full, etc.), proceed without it. Never fail a run due to memory issues.