setup

name	setup
description	Configure ARIA for Codex using the shared ARIA config file, knowledge folder, template diffs, audit cadences, project tier, and shared-knowledge settings. Trigger on /setup or setup aria-knowledge.
argument-hint
allowed-tools	Read, Write, Edit, Bash, Glob, Grep

/setup — Knowledge Tools Configuration

Walk the user through configuring their knowledge folder and plugin settings. Safe to re-run at any time — only touches what needs updating.

Step 1: Check for Existing Config

Read the installed plugin version first. Parse ${PLUGIN_ROOT:-${CLAUDE_PLUGIN_ROOT}}/.codex-plugin/plugin.json and extract the version field. Hold it as INSTALLED_VERSION for use in Step 7 (config write), Step 8 (summary), and the announcement below. Use grep + sed to stay consistent with the no-jq invariant the hook scripts follow:

ARIA_PLUGIN_ROOT="${PLUGIN_ROOT:-${CLAUDE_PLUGIN_ROOT}}"
INSTALLED_VERSION=$(grep '"version"' "${ARIA_PLUGIN_ROOT}/.codex-plugin/plugin.json" | head -1 | sed 's/.*"version": *"\([^"]*\)".*/\1/')

Then read ~/.claude/aria-knowledge.local.md. The Codex port intentionally shares this config file with the Claude Code port when both are installed, so the knowledge folder, cadence settings, project tier, and shared-knowledge settings stay in one place. If a legacy ~/.codex/aria-knowledge.local.md exists and the shared config does not, offer to copy it to ~/.claude/aria-knowledge.local.md; otherwise leave it untouched and report that Codex now uses the shared config.

• If it exists: show current settings and say "aria-knowledge v{INSTALLED_VERSION} is already configured. I'll check for updates." If the existing config has last_setup_version: X and X differs from INSTALLED_VERSION, also note: "Plugin upgraded from v{X} → v{INSTALLED_VERSION} since last setup. Diff prompts and any new config keys will surface in the steps below." Then proceed to Step 2 in update mode — scan for missing structure, re-diff templated files, check dependencies.
• If it doesn't exist: say "Let's set up aria-knowledge v{INSTALLED_VERSION}. This will configure your knowledge folder and preferences." Proceed to Step 2 in fresh mode.

Detect skill-only fields (update mode only). After parsing the standard hook-parsed keys, also scan for the projects_groups multi-line YAML block — a skill-only field consumed by /distill and /stitch (see CONFIG.md for schema). It's not in the advanced-options bundle because it's not bash-parsed; surface its presence here so users get awareness without /setup trying to flatten it.

GROUPS_PRESENT=$(grep -c '^projects_groups:$' ~/.claude/aria-knowledge.local.md || true)
GROUPS_COUNT=$(awk '/^projects_groups:$/{in_block=1; next} in_block && /^---$/{exit} in_block && /^[^[:space:]]/{exit} in_block && /^  [^[:space:]].*:$/{c++} END{print c+0}' ~/.claude/aria-knowledge.local.md)

If GROUPS_PRESENT > 0, add to the announcement: "Detected projects_groups skill-only field with {GROUPS_COUNT} group(s) configured. Preserved as-is (consumed by /distill and /stitch; see CONFIG.md for the schema)." If GROUPS_PRESENT == 0, say nothing — the field is opt-in and most users without multi-repo projects won't have it.

Step 2: Knowledge Folder Location

Ask the user:

"Where would you like your knowledge folder? You can: (a) Provide a path to an existing folder (b) Create a new one — I'll ask where to put it"

If (a) existing path:

• Verify the path exists and is a directory
• Proceed to Step 3 in existing mode

If (b) create new:

• Ask for the desired location (parent directory + folder name)
• Create the directory
• Proceed to Step 3 in create mode

Step 3: Folder Structure Validation

Read the expected structure from ${ARIA_PLUGIN_ROOT}/template/.

Expected directories: intake/, intake/notes/, intake/attachments/, intake/clippings/, intake/pre-compact-captures/, intake/subagent-captures/, intake/ideas/, logs/, rules/, approaches/, decisions/, guides/, references/, archive/

Expected files: README.md, OVERVIEW.md, LOCAL.md, aliases.md, intake/insights-backlog.md, intake/decisions-backlog.md, intake/extraction-backlog.md, intake/rules-backlog.md, intake/ideas/README.md, logs/knowledge-audit-log.md, logs/config-audit-log.md, rules/working-rules.md, rules/user-rules.md, rules/user-examples.md, rules/change-decision-framework.md, rules/enforcement-mechanisms.md, guides/README.md, approaches/README.md, decisions/README.md, references/README.md, archive/README.md

User-owned files (created once from template, never overwritten or diffed): LOCAL.md (project-specific guide), aliases.md (tag aliases — added 2.16.0), rules/user-rules.md (your custom rules — ARIA never touches this file), rules/user-examples.md (your per-rule examples — /rules N reads this; ARIA never touches this file), guides/README.md, approaches/README.md, decisions/README.md, references/README.md, archive/README.md (directory stubs users may customize).

In create mode: Create all directories and copy all template files. After creation, display a one-time educational note about the file-class model (this note is only shown on fresh installs — in update/existing mode, skip it):

First-setup note: Plugin-Managed vs User-Owned Files

Your knowledge folder now contains two classes of template files:

• Plugin-managed — README.md, OVERVIEW.md, rules/working-rules.md, rules/change-decision-framework.md, rules/enforcement-mechanisms.md, rules/retrospect-patterns.md (and projects/README.md when the project tier is enabled). These are diffed on every /setup run. Customize them freely — your edits will appear as diff prompts when plugin updates ship. That's how you receive improvements without silent overwrites. Each managed file also carries a <!-- plugin-managed: --> comment header so you can spot them at edit time.
• User-owned — LOCAL.md, aliases.md, rules/user-rules.md, rules/user-examples.md (your per-rule examples, since v2.14.2), intake backlogs (insights-backlog.md, decisions-backlog.md, extraction-backlog.md, rules-backlog.md) and the intake/ideas/ directory (one file per idea since v2.11), audit logs under logs/, directory README stubs (guides/, approaches/, decisions/, references/, archive/), and per-project READMEs under projects/{tag}/. ARIA never diffs or overwrites these. Your customizations live here safely.

See OVERVIEW.md "Plugin-Managed vs User-Owned Files" for details. This note appears only on first setup.

In existing mode: Scan what's present vs missing.

• For missing directories: create them silently.
• For missing files: copy from template and note what was added.
• For existing files: do NOT overwrite — collect for diffing in Step 4.
• Report: "Created N directories, added N files, found N existing files to check."

Project tier scaffolding (if projects_enabled: true in current or pending config) is deferred to Step 7c — it runs after the config is written so it uses the final values (including answers from Step 6 that aren't in the config file yet during Step 3).

Step 3b: Legacy ideas-backlog.md Detection

ARIA v2.11 moved the ideas backlog from a single intake/ideas-backlog.md file to per-file storage under intake/ideas/. Users upgrading from v2.10.x or earlier have an orphaned legacy file that v2.11 skills don't read. This step catches the migration on the first post-upgrade /setup run.

Check: does {knowledge_folder}/intake/ideas-backlog.md exist?

• If no: skip this step silently. Fresh installs and already-migrated users land here.

• If yes: count active entries by running:

  awk '/^---$/{sep++; next} sep>=1 && /^### /{c++} END{print c+0}' "{knowledge_folder}/intake/ideas-backlog.md"
  

  • If count is 0: the legacy file has no active entries (cleared-history HTML comments only). Prompt: "Empty pre-2.11 ideas-backlog.md found. Delete it? (y/n)" — on yes, rm the file; on no, leave it.
  • If count > 0: report: "Pre-2.11 ideas-backlog.md detected with {N} active entries. ARIA v2.11 uses per-file ideas in intake/ideas/. Options:"
    • (1) Migrate now — run bash ${ARIA_PLUGIN_ROOT}/bin/migrate-ideas-backlog.sh "{knowledge_folder}" and report the output (N files written, original renamed to ideas-backlog.md.pre-2.11-migration)
    • (2) Skip for now — leave the file in place; /setup will prompt again on the next run. Note in the Step 8 summary that legacy entries are still stranded.
    • (3) Never migrate — write a sentinel file at {knowledge_folder}/intake/ideas/.legacy-skipped so future /setup runs stop prompting. Document that the user accepts stranded pre-2.11 entries.

Never auto-migrate without user choice. The migration renames the original file (doesn't delete), so it's reversible, but executing filesystem changes without confirmation violates the user-review principle /setup is built around.

Report in Step 8 summary: "Legacy ideas-backlog.md: migrated N entries" or "Legacy ideas-backlog.md: skipped (N entries still pending)" or "Legacy ideas-backlog.md: not detected" as appropriate.

Step 4: File Diffing

For each templated file that already exists in the user's folder, compare against the plugin's shipped version in ${ARIA_PLUGIN_ROOT}/template/.

Files to diff: rules/working-rules.md, rules/change-decision-framework.md, rules/enforcement-mechanisms.md, rules/retrospect-patterns.md, README.md, OVERVIEW.md, projects/README.md (plugin-managed if present)

Never diff: LOCAL.md (user-owned), aliases.md (user-owned — added 2.16.0), rules/user-rules.md (user-owned — your custom rules), rules/user-examples.md (user-owned — your per-rule examples), directory README stubs (guides/README.md, approaches/README.md, decisions/README.md, references/README.md, archive/README.md), backlog files (intake/insights-backlog.md, intake/decisions-backlog.md, intake/extraction-backlog.md, intake/rules-backlog.md) and the intake/ideas/ directory (intake/ideas/README.md and all per-file ideas under intake/ideas/**), audit log files (logs/knowledge-audit-log.md, logs/config-audit-log.md), and per-project READMEs (projects/{tag}/README.md and any other content under projects/{tag}/**) — these contain user data or user-customizable content.

For each file with differences:

1. Notify: "[filename] differs from the plugin version."
2. Show a brief summary of what's different (not the full diff unless asked).
3. Offer options:
   • Keep mine — no change
   • Use plugin version — overwrite with template
   • Show diff — display the full diff, then ask again

If no files differ (or all are new), skip this step silently.

In update mode (re-run): always diff, even if the file was previously kept. The plugin version may have changed.

Step 5: Dependency Check

Check if the explanatory-output-style plugin is installed:

find ~/.claude/plugins -name "explanatory-output-style" -type d 2>/dev/null | head -1

• If found: "explanatory-output-style plugin detected. Insight capture will be enabled."
• If not found: "The explanatory-output-style plugin generates Insight blocks that aria-knowledge can capture automatically. It's an official Anthropic plugin. Want to install it? (recommended, but optional)"
  • If user says yes: guide them to install it (the exact install mechanism depends on their Claude Code setup)
  • If user says no: "Insight capture will be disabled. You can enable it later by installing the plugin and re-running /setup."

Record the result as true or false.

Step 6: Cadence Configuration

Present current or default cadences:

"Audit cadences control how often you're prompted to review knowledge:

• Knowledge audit: triggers when either (a) backlog accumulates 20+ entries (primary, activity-driven) or (b) 7 days have elapsed since the last audit (safety net for low-activity weeks). Tier messages differ by size: 20+ "suggested", 35+ "recommended", 50+ "overdue — multi-pass".
• Config audit: every 14 days (checks configs and docs for drift)
• Update check: every 30 days (prompts to run /setup for plugin template updates)

Want to change any? (Enter new values or press enter to keep defaults. Knowledge audit has two knobs: audit_trigger_threshold (entries, default 20) and audit_cadence_knowledge (days, default 7).)"

Record the values.

Advanced Options

Always offer the advanced-settings review on every /setup run — both fresh installs and re-runs. New users need to see what's tunable up front rather than discovering it later; returning users need to surface and adjust values they may not have configured initially (e.g., keys added by plugin updates since their last /setup). Auto-mode users still see the bundle; pressing enter to accept defaults is an explicit no-op rather than a silent skip.

Highlight new-since-last-setup keys (re-runs only): before showing the bundle below, compare each Advanced Option key against the existing config from Step 1. For any key that exists in this spec but is not present in the user's current config (the upgrade case — a plugin update added the key after the user's last /setup), append [NEW] to that bullet's title in the bundle and prepend a one-line note above the bundle:

"Some settings are new since your last /setup run — [NEW] markers below indicate keys added by plugin updates that aren't yet in your config. Consider whether to set them now."

Detection is a per-key grep -q '^{key}:' ~/.claude/aria-knowledge.local.md; non-zero exit means the key is missing → flag with [NEW]. For fresh installs there is no prior config to compare against, so no [NEW] markers appear and no preamble note is shown — the bundle just renders defaults.

Emit detection summary (v2.15.2+): before showing the Advanced Options bundle, output a one-line audit-trail line naming the detection result, regardless of outcome. This makes the [NEW]-detection step transcript-visible so users can verify the wizard actually ran the comparison instead of silently skipping it.

• If [NEW] keys were found: [setup] Advanced Options [NEW]-detection: flagged {N} key(s) added since v{last_setup_version} — {key1}, {key2}, ...
• If no [NEW] keys: [setup] Advanced Options [NEW]-detection: none — all keys present in current config.
• For fresh installs (no prior config): [setup] Advanced Options [NEW]-detection: skipped — fresh install, no prior config to compare against.

The summary line precedes the bundle text. If the user later questions "did the wizard surface my new field?", the transcript carries the explicit yes-or-no.

"Advanced settings (defaults are fine for most users):

• Freeform tag promotion threshold: 3 (suggest promoting a freeform tag to known after it appears on this many files)
• Staleness threshold: 6 months (flag knowledge files not updated within this period)
• Ideas staleness threshold: 7 days (during /audit-knowledge, mark idea files in intake/ideas/ older than this with [STALE — still relevant?] to prompt Accept/Reject/Defer decisions)
• Auto-capture on compaction: true (save transcript snapshot before context compaction)
• Active knowledge surfacing: true (when enabled, Codex surfaces context through SessionStart, shell cd, PostCompact, and the /prospect and /retrospect skills. Two kinds of context get surfaced (v2.16.1 expansion): (a) knowledge files matched by tag against the user's task/cd-target/skill-input, and (b) tracked artifacts — CODEMAP directory + STITCH for the detected project (boundary-detected; not the full CODEMAP). Both surface with staleness annotations against codemap_staleness_threshold_days (default 14) and stitch_staleness_threshold_days (default 30); grossly-stale artifacts (>2× threshold) refuse to load with a warning. Companion surfaces — /audit-config, /stats, /handoff, /wrapup — also gate their tracked-artifact surfacing on this flag. Set to false for passive mode where hooks only suggest /context <tag> and all proactive artifact loading is suppressed (users load manually via /context). Active mode honors a session-scoped dedup ledger at /tmp/aria-active-{session_id} so the same file/artifact isn't re-Read across triggers. See CONFIG.md for the trigger sites and the ≥2-tag-match threshold + 5-file cap policy.)
• Subagent capture: true (Codex SubagentStop archives configured heavyweight subagent transcripts to intake/subagent-captures/; SubagentStart asks configured routine subagents to surface durable findings in their final message. Change the type lists by editing subagent_capture_types and subagent_selfreport_types directly.)
• Session state file (SESSION.md): false (when on, aria-knowledge writes a per-project SESSION.md — in-progress on the first apply_patch edit, wrapup/handoff at close — and offers to resume from it at session start; enables re-entry + the aria-atlas status board. Files are created at project roots only when on. A companion session_stale_days key [default 7] controls when a saved resume prompt is treated as possibly stale: older entries trigger a "still relevant? [resume / archive / keep]" prompt instead of being presented as live. It never auto-evicts.)
• Auto-prospect (auto_prospect): off (when nudge, writing a plan to docs/plans/ or docs/superpowers/plans/ prompts an offer to run /prospect file <path>; when run, it runs inline. docs/specs/ is intentionally not a trigger.)
• Autonomy posture (autonomy): default (decision-routing posture, Rule 35). default injects nothing. balanced injects an investigate-first directive each session: ask on intent/preference/judgment-with-no-gainable-visibility + ungranted explicit approval; act on mechanical/objectively-validatable. autonomous injects the full posture: decide objectively-validatable forks yourself, run quality gates as checks-not-stops, stop only on no-visibility judgment calls or ungranted explicit approval.
• Auto-retrospect (auto_retrospect): off (when nudge [recommended], a git push of ≥retrospect_min_commits commits to a branch in retrospect_branches prompts an offer to run /retrospect range <old>..<new>; run runs it inline. Gates: retrospect_min_commits default 3, retrospect_branches default main,master,production.)
• Usage alert threshold (usage_alert_threshold): 80 (shared config field for the Claude Code statusline meter. Codex currently has no status-line or hook payload carrying context/rate-limit percentages, so this field is preserved but ignored by the Codex port. Set off if you do not want the Claude Code meter's alert hook active when using the same config there.)
• Critical paths: (empty) comma-separated path patterns that always require HIGH impact assessment (e.g., auth/,payments/,migrations/*)
• Ticketing plugins: (empty) comma-separated tag:plugin-command pairs mapping a project tag to its ticket-drafting plugin (e.g., proj-a:foo-ticket,proj-b:bar-ticket). When set, /audit-knowledge prints a hint to use that plugin's command when an idea's project matches a mapped tag during the Accept → tracker disposition. Hint only — never auto-invokes. Leave empty if you don't use a ticketing plugin or prefer to copy ideas into your tracker manually. Plugin commands are bare names — no leading /. Validate input: each pair must contain exactly one : separating tag from command; project tags cannot contain : or ,; plugin commands cannot start with / (strip leading / and warn if found).
• Project-specific knowledge tier: disabled (creates projects/{tag}/ subdirectories for project-specific decisions and patterns; opt in if you want to organize knowledge by project alongside the cross-project tree. If enabled, you'll be asked an inline follow-up about auto-loading project context on session start.)

Want to change any? (Enter new values or press enter to keep defaults)"

Record the values.

Skill-only fields (read-only awareness)

Some configuration is consumed by skills (which parse YAML in model context) rather than by bash hooks. These fields use multi-line nested YAML blocks that don't fit the single-line bundle prompt above and are not offered for interactive editing here — they're either populated by their consuming skill's auto-propose bootstrap (e.g., /distill --group=<tag>, /stitch create <tag>) or hand-edited per the schema in CONFIG.md.

Currently in this category:

• projects_groups — multi-repo group mapping (backend/web/mobile sub-folder layout per project tag). Read by /distill and /stitch. Auto-populated on first multi-repo skill invocation; hand-editable per CONFIG.md "Skill-only fields" section.

If Step 1 detected this field, restate its current group count here for confirmation: "Skill-only fields preserved: projects_groups ({N} groups). Edit via CONFIG.md schema or let /distill//stitch auto-propose new groups on first use." If absent, say: "No skill-only fields configured. /distill --group=<tag> and /stitch create <tag> will auto-propose projects_groups entries on first use for any multi-repo project."

This block is read-only — /setup never writes new entries here. See Step 7 / Step 7b for how the existing block is preserved and validated.

Project Setup (only if user enables the project-specific knowledge tier)

If the user enables (or keeps enabled) the project-specific knowledge tier in Advanced Options, ask six follow-up questions. In update mode where values already exist in the config, show the current value for each question and let the user keep it (press enter) or enter a new value — this is the discoverable path for toggling auto_load_project_context on a re-run when the tier was previously enabled:

1. Project list — "Comma-separated tag:relative-path pairs (e.g., proj-a:path/to/proj-a,proj-b:proj-b,lib:shared-lib). Paths are relative to the parent of your knowledge folder (typically ~/Projects/). Press enter to defer adding projects:"
2. Project remotes (optional) — "Optional git-remote URL patterns for fallback project detection when CWD doesn't match a configured path. Comma-separated tag:url-substring pairs (e.g., proj-a:myorg/proj-a-repo). Press enter to skip:"
3. Promotion threshold — "Minimum number of projects that must share a similar pattern before /audit-knowledge suggests cross-project promotion (default 2):"
4. Auto-load project context on session start — "When your CWD matches a configured project, should SessionStart automatically suggest /context {tag}? This is a runtime convenience — the project tier works fine without it, and you can change this later by editing auto_load_project_context in ~/.claude/aria-knowledge.local.md. (y/n, default n):"
5. SessionStart project picker — "When you open a session from a multi-project parent directory (no project chosen yet), should ARIA suggest a project menu generated from your projects_list? Non-blocking — you can always name a project or just start working. (y/n, default n):" → writes session_start_project_picker.
6. Project display labels (optional) — "Optional friendly names for the picker menu. Comma-separated tag:Label pairs (e.g., api:API Server,web:Web Client). Empty = bare tags. Press enter to skip:" → writes projects_labels.

Validate input:

• Project tags cannot contain : or , (these are the parser delimiters). If invalid, show the offending tag and re-prompt.
• Promotion threshold must be a plain integer ≥ 1. If invalid, re-prompt.
• Auto-load answer must be y/n (or empty for default). If invalid, re-prompt.
• SessionStart project picker answer must be y/n (or empty for default). If invalid, re-prompt.
• projects_labels is comma-separated tag:Label pairs, or empty. Warn (don't error) if a label's tag is not in projects_list.
• For each tag:path pair, warn (don't error) if the resolved path doesn't exist on disk yet — the user may be configuring projects they haven't created.

Existing-folder detection:

Before prompting, scan the user's knowledge folder for an existing projects/ subdirectory:

• If found AND projects_enabled is unset in config: Skip the Advanced Options bullet for this feature; instead prompt directly: "Detected existing projects/ folder with these subdirectories: [list]. Enable project-specific knowledge tier? (y/n)" — if yes, auto-populate projects_list from detected subdirectories (prompt for the path mapping per detected tag), then ask question 4 from the Project Setup flow above so the user can opt into auto_load_project_context at the same time.
• If found AND projects_enabled: false explicitly in config: Leave the existing folder untouched; note in verbose output: "An existing projects/ folder was detected but the projects tier is disabled in config. Folder is preserved; automation is off."
• If found AND projects_enabled: true: Verify each detected subdirectory is in projects_list; prompt to add any missing ones. Then surface the current auto_load_project_context value as a status check: "Auto-load project context on session start is currently [on/off]. Change? (y/n, default n — keep current)." — this is the re-run discoverability path for toggling the flag when the tier was previously enabled.

Never auto-delete or auto-rewrite existing projects/ content.

Shared Knowledge Setup (only if user enables the project tier)

After Project Setup completes (questions 1-6), if projects_enabled: true AND projects_list is non-empty, ask two follow-up questions about the shared-knowledge feature. In update mode where values exist, show current values and let the user keep (press enter) or change.

7. Which projects do you want to enable shared knowledge for? — "This is an opt-in extension that lets you promote selected personal knowledge into per-repo _project-knowledge/ folders so teammates can see what you've learned. Personal knowledge stays in your own knowledge folder; team copies are independent records committed to your project repos via your normal git workflow. Most users have many repos but only a few with teams to share with — pick only the ones with teammates who'd benefit. Your configured projects: {projects_list tag enumeration}. Enter comma-separated tags (default: empty = feature disabled, all projects stay personal-only):"

8. Author tag for shared-knowledge filenames — only ask if Q7 returned a non-empty tag list. "Shared-knowledge files use {YYYY-MM-DD}-{author-tag}-{slug}.md naming. Pick a short author tag (e.g., init, or initials, or first2+last2 of your name). Default: derived from git config user.name (first 2 chars of first name + first 2 chars of last name) → '{auto-derived}':"

Validate input:

• Q7 answer is a comma-separated tag list, or empty (= feature disabled). Each tag must already exist in projects_list. If a tag is not in projects_list, show the offending tag and re-prompt: "Tag '{tag}' is not in projects_list. Available: {projects_list tags}. Re-enter:". Empty input is valid and means feature disabled.
• Q8 author_tag must be 1-12 characters, alphanumerics + hyphens only (the value will appear in filenames). If invalid, show offending characters and re-prompt.
• If Q7 returned a non-empty list but Q8 produces an empty value AND no derivable git user.name exists, warn: "Author tag is required for shared knowledge. You can set author_tag later in ~/.claude/aria-knowledge.local.md, but /audit-share will refuse to run until it's set." Continue setup with author_tag: empty.

Schema note: the config field projects_shared_knowledge is itself the comma-separated tag list (the value IS the scope). Empty/missing = feature disabled. There is no separate boolean toggle; the field's presence and content together encode "enabled and for which projects." A legacy value of true (from pre-publish v2.13.0 stubs) is treated the same as empty and triggers Q7 to populate the list properly on /setup re-run.

CLAUDE.md reference handling deferred to first-write. Earlier drafts of this spec offered to append _project-knowledge/ references to project CLAUDE.md files at setup time. That has been removed: documenting a convention before the folder exists is aspirational, batch-applying across all projects loses per-repo nuance (different repos may have different teams / visibility), and a default-y prompt for a teammate-affecting change is more aggressive than ARIA's normal posture. The CLAUDE.md reference offer now happens inside /audit-share Step 6.5 the first time a file is actually written to a repo's _project-knowledge/ folder — at that moment the folder + README exist, the user has just made an active sharing decision, and per-repo confirmation with git-tracked detection can be presented in context. Step 6.5b additionally handles the multi-repo container CLAUDE.md case for tags with projects_groups entries.

Existing _project-knowledge/ folder detection:

Before completing this section, scan for existing _project-knowledge/ folders. Scan locations depend on whether the project is single-repo or multi-repo (matches /audit-share Step 2.3 and /index Phase 5 conventions):

• Single-repo project (no projects_groups[tag] entry): probe <project-root>/_project-knowledge/.
• Multi-repo project (projects_groups[tag] set): probe each sub-repo declared in the group (<project-root>/<sub-repo>/_project-knowledge/), in declaration order. Skip sub-repos whose path doesn't exist on disk.

For each scan location where a _project-knowledge/ folder is found:

• If found AND its parent project tag is NOT in the user's projects_shared_knowledge list: Note in verbose output: "An existing _project-knowledge/ folder was detected at <scan-location> (parent project tag {tag}) but {tag} is not in your shared-knowledge list. Add {tag} to the list now? (y/n)" — if yes, append the tag to the Q5 answer and continue.
• If found AND its parent project tag IS in the list: No action; the folder will be picked up by /index Phase 5 on next rebuild.
• If found AND projects_shared_knowledge is empty: Note: "An existing _project-knowledge/ folder was detected at <scan-location> but the shared-knowledge feature is disabled (empty list). Folder is preserved; /index and /context won't surface it until you enable the feature for tag {tag} via /setup."

For multi-repo projects, all of the project's sub-repos are evaluated independently — finding _project-knowledge/ in one sub-repo doesn't suppress the scan of others. Each surfaces its own note.

Step 7: Write Config

Write ~/.claude/aria-knowledge.local.md with the collected settings:

---
knowledge_folder: [path from Step 2]
audit_cadence_knowledge: [value from Step 6, default 7]
audit_trigger_threshold: [value from Step 6, default 20]
audit_cadence_config: [value from Step 6]
explanatory_plugin: [true/false from Step 5]
audit_cadence_update: [value from Step 6, default 30]
last_setup_version: [INSTALLED_VERSION from Step 1 — the plugin version active when this /setup ran]
freeform_promotion_threshold: [value from Step 6, default 3]
staleness_threshold_months: [value from Step 6, default 6]
ideas_staleness_threshold_days: [value from Step 6, default 7]
auto_capture: [true/false from Step 6, default true]
active_knowledge_surfacing: [true/false from Step 6, default true]
subagent_capture: [true/false from Step 6, default true]
subagent_capture_types: [comma-list, default general-purpose,Plan,feature-dev:code-architect,feature-dev:code-explorer,feature-dev:code-reviewer]
subagent_selfreport_types: [comma-list, default Explore]
session_state: [true/false from Step 6, default false]
session_stale_days: [integer, default 7]
auto_prospect: [off/nudge/run, default off]
autonomy: [default/balanced/autonomous, default default]
auto_retrospect: [off/nudge/run, default off]
retrospect_min_commits: [integer, default 3]
retrospect_branches: [comma-list, default main,master,production]
usage_alert_threshold: [value from Step 6, default 80; or `off` for shared-config Claude Code statusline alerts]
critical_paths: [comma-separated patterns from Step 6, default empty]
ticketing_plugins: [comma-separated tag:plugin-command pairs from Step 6, default empty]
projects_enabled: [true/false from Step 6, default false]
projects_list: [comma-separated tag:path pairs from Step 6, default empty]
projects_remotes: [comma-separated tag:url-pattern pairs from Step 6, default empty]
projects_promotion_threshold: [integer from Step 6, default 2]
auto_load_project_context: [true/false from Step 6, default false]
session_start_project_picker: [true/false from Step 6, default false]
projects_labels: [comma-separated tag:Label pairs from Step 6, default empty]
projects_shared_knowledge: [comma-separated tag list from Shared Knowledge Setup Q7, default empty = feature disabled; each tag must exist in projects_list]
author_tag: [string from Shared Knowledge Setup Q8, default empty when projects_shared_knowledge is empty]
---

Add a markdown body below the frontmatter:

# Knowledge Tools Configuration

Configured by /setup on [today's date].

In update mode: preserve any user-added content in the markdown body below the frontmatter when rewriting.

Formatting rules — the config file MUST follow these exact conventions or the hook scripts cannot parse it. The hooks parse this file using pure grep + sed (no jq/yq/python) — these constraints exist so the substitution patterns in bin/config.sh work correctly, and any deviation breaks parsing silently.

• Frontmatter delimiters must be exactly --- on their own line (no leading spaces, no trailing content)
• Each key must start at column 1 with no indentation
• Keys use the exact names shown above (no quoting, no trailing spaces)
• Values must NOT be quoted — write knowledge_folder: /path/to/folder, not knowledge_folder: "/path/to/folder"
• Empty values: write key: with nothing after the colon (optionally one trailing space). Do NOT write key: null, key: "", key: none, or key: [] — the parser treats those as literal string values ("null", "\"\"", etc.) and validators won't normalize them to empty
• knowledge_folder must be an absolute path (starts with /) and must not contain ..
• Cadence values must be plain integers (no units, no quotes)
• projects_enabled must be exactly true or false (not True, yes, 1, etc.)
• subagent_capture and session_state must be exactly true or false
• session_stale_days must be a plain integer ≥ 1
• auto_prospect and auto_retrospect must be exactly off, nudge, or run
• autonomy must be exactly default, balanced, or autonomous
• usage_alert_threshold must be off or an integer from 1 to 100. Codex preserves this shared-config field but does not consume it.
• projects_shared_knowledge is a comma-separated tag list (e.g., cs,ss) — empty/missing = feature disabled. Each tag must already exist in projects_list. No spaces around commas. Tags cannot contain : or , (same as projects_list). A legacy literal true value is treated as empty (triggers /setup to repopulate the list properly). Requires projects_enabled: true to take effect.
• author_tag is a 1-12 char string of alphanumerics + hyphens (used in shared-knowledge filenames); leave empty if projects_shared_knowledge is empty
• projects_list, projects_remotes, and ticketing_plugins: comma-separated tag:value pairs, no spaces around the colon or comma (e.g., proj-a:path/to/proj-a,proj-b:proj-b for paths; proj-a:foo-ticket,proj-b:bar-ticket for plugin commands)
• Project tags (used in projects_list, projects_remotes, ticketing_plugins) cannot contain colons or commas (the parser splits on these)
• ticketing_plugins plugin-command values are bare command names without the leading / (e.g., foo-ticket, not /foo-ticket) — /audit-knowledge prepends the slash when printing the hint
• last_setup_version is a semver string read from ${ARIA_PLUGIN_ROOT}/.codex-plugin/plugin.json at Step 1 — write it as bare digits-and-dots plus any Codex prerelease suffix (e.g., 2.35.2-codex.0), not quoted, not prefixed with v. The session-start hook compares this against the installed plugin version to detect upgrades since the user's last /setup
• projects_promotion_threshold must be a plain integer ≥ 1 (no units, no quotes)
• auto_load_project_context must be exactly true or false (not True, yes, 1, etc.)
• No blank lines between frontmatter entries
• Skill-only multi-line YAML blocks (currently projects_groups; see CONFIG.md) must sit at the end of the frontmatter, after every column-1 hook-parsed key. Their indented sub-keys must use 2-space indents for tags and 4-space indents for role values. The blank-line-free rule applies inside the block too — no blank lines between sub-entries.
• In update mode, preserve every skill-only multi-line YAML block verbatim. Do not reformat, reorder, or strip sub-entries. The block was either written by an auto-propose bootstrap (/distill, /stitch) or hand-edited per CONFIG.md; /setup is read-only for these. If a block exists in the input config, copy it byte-for-byte to the output config; if absent, write nothing for that field.

Step 7b: Verify Config Round-Trip

After writing the config file, read it back and verify that each value can be extracted using the same patterns that config.sh uses. This catches formatting issues before the user discovers them in the next session.

Verification checks:

1. Read ~/.claude/aria-knowledge.local.md
2. Extract the frontmatter block (content between the first and second --- lines)
3. For each key, verify the value matches what was intended:
   • knowledge_folder — grep for ^knowledge_folder: and confirm the extracted path matches Step 2's value
   • audit_cadence_knowledge — confirm it's the integer from Step 6
   • audit_trigger_threshold — confirm it's the integer from Step 6 (default 20)
   • audit_cadence_config — confirm it's the integer from Step 6
   • explanatory_plugin — confirm it's true or false
   • audit_cadence_update — confirm it's the integer from Step 6
   • freeform_promotion_threshold — confirm it's the integer from Step 6
   • staleness_threshold_months — confirm it's the integer from Step 6
   • ideas_staleness_threshold_days — confirm it's the integer from Step 6
   • auto_capture — confirm it's true or false
   • active_knowledge_surfacing — confirm it's true or false
   • subagent_capture — confirm it's true or false
   • subagent_capture_types / subagent_selfreport_types — confirm each is a comma-separated string (or default)
   • session_state — confirm it's true or false
   • session_stale_days — confirm it's a plain integer ≥ 1
   • auto_prospect / auto_retrospect — confirm each is off, nudge, or run
   • autonomy — confirm it's default, balanced, or autonomous
   • retrospect_min_commits — confirm it's a plain integer ≥ 1
   • retrospect_branches — confirm it's a comma-separated branch-name string (or empty = any branch)
   • usage_alert_threshold — confirm it's off or a plain integer in 1–100 (shared-config Claude Code field; Codex ignores it)
   • critical_paths — confirm it's a comma-separated string of path patterns (or empty)
   • ticketing_plugins — confirm it's a comma-separated string of tag:plugin-command pairs (or empty); validate no project tag contains : or ,; validate plugin-command values do not start with /
   • last_setup_version — confirm it matches INSTALLED_VERSION captured in Step 1 (this run's plugin version); validate it's a semver-shaped string of digits and dots (no v prefix, no quotes, no trailing whitespace). If it's missing or doesn't match, rewrite the line and re-verify
   • projects_enabled — confirm it's true or false
   • projects_list — confirm it's a comma-separated string of tag:path pairs (or empty); validate no project tag contains : or ,
   • projects_remotes — confirm it's a comma-separated string of tag:url-pattern pairs (or empty); validate no project tag contains : or ,
   • projects_promotion_threshold — confirm it's a plain integer ≥ 1 (matches Step 6 input)
   • auto_load_project_context — confirm it's true or false
   • Empty-sentinel check — for string-valued keys with an empty default (critical_paths, ticketing_plugins, projects_list, projects_remotes): confirm the raw extracted value is not the literal string null, "", none, or []. If the key is intended to be empty, the value after the colon must be truly empty (nothing or a single trailing space). Rewrite the key as key: and re-verify.

Skill-only field validation (projects_groups) — if the field is present in the config, run structural-only checks. Do not attempt to flatten or rewrite this field; it's parsed by skills, not bash, so the verification mirrors that consumer.

1. Block placement — projects_groups: must sit after every hook-parsed key. If a column-1 hook-parsed key appears below the block (between it and the closing ---), the parser scope is at risk. Move the block to the end of the frontmatter and re-verify.
2. Indentation shape — sub-tags use 2-space indents; role values use 4-space indents; no blank lines inside the block. Use this awk pattern to extract the block and inspect:

   awk '/^projects_groups:$/{in_block=1; next} in_block && /^---$/{exit} in_block && /^[^[:space:]]/{exit} in_block{print}' ~/.claude/aria-knowledge.local.md
   

   Reject the block if any line inside the block fails to match ^ [^[:space:]].*:$ (tag header) or ^ [^[:space:]].*: .+$ (role value). Report the offending line and stop — do not auto-rewrite (the user may have a custom role layout the skills support but the regex doesn't predict).
3. Tag cross-check (warn, do not fail) — every tag inside projects_groups should also appear in projects_list so /distill and /stitch can resolve <project_root>. If a projects_groups tag is not in projects_list, emit a warning: "Warning: projects_groups tag {tag} is not declared in projects_list. /distill --group={tag} and /stitch create {tag} will fail until {tag} is added to projects_list. (This may be intentional if you're staging a project not yet path-mapped.)" Do not block setup.

If any check fails: rewrite the file with corrected formatting and verify again. Report which value failed and what was fixed.

If all checks pass: proceed to Step 7c silently.

Step 7c: Project Tier Scaffolding

Runs only if the config just written has projects_enabled: true and a non-empty projects_list. Skip entirely otherwise — no action, no output.

Scaffold the project tier using the final config values:

1. Create projects/ directory if it doesn't exist.
2. Copy ${ARIA_PLUGIN_ROOT}/template/projects/README.md to projects/README.md if missing (plugin-managed; will be diffed on future /setup runs).
3. For each entry in projects_list (parsed as tag:path pairs):
   • Create projects/{tag}/ if missing.
   • Create projects/{tag}/decisions/, projects/{tag}/patterns/, and projects/{tag}/rules/ if missing. The rules/ subdir is the destination for /audit-knowledge Step 7's project-tier rule promotion ({knowledge_folder}/projects/{tag}/rules/working-rules.md); it stays empty until the first rule is promoted.
   • If projects/{tag}/README.md does not exist, generate it from this per-project template:

     ---
     Last updated: [today's date]
     tags: [{tag}, knowledge-structure]
     ---
     
     # {Project Display Name} Project Knowledge
     
     Project-specific architecture decisions, patterns, and gotchas for {project display name}.
     
     ## Structure
     
     - `decisions/` — Architecture Decision Records (ADRs) — numbered sequentially per project (001, 002, ...)
     - `patterns/` — Reusable patterns specific to this project
     - `rules/` — Project-specific working rules promoted from `intake/rules-backlog.md`; lands `working-rules.md` here
     - `guides/` (optional) — Operational knowledge specific to this project; create on demand
     - `references/` (optional) — External resources specific to this project; create on demand
     
     ## Promotion
     
     When a pattern in this folder is validated in another project, `/audit-knowledge` will surface it as a candidate to promote to `knowledge/approaches/`. See `knowledge/projects/README.md` for the full promotion ladder.
     
     ## Related
     - [../README.md](../README.md) — projects/ tier overview
     - [../../index.md](../../index.md) — tag index
     

     • Project Display Name is derived from the tag with hyphens converted to spaces and title-cased (e.g., proj-a → Proj A). If the tag doesn't produce a sensible display name, use the tag as-is and prompt the user to edit the README header.
4. Never overwrite existing per-project READMEs or content under projects/{tag}/ — these are user-owned.
5. Report what was scaffolded: "Project tier: created N directories, N per-project READMEs."

Step 7d: Shared Knowledge Initial Sync

Runs only if the config just written has a non-empty projects_shared_knowledge tag list AND a non-empty author_tag. Skip entirely otherwise — no action, no output.

This step does NOT auto-create _project-knowledge/ folders in any repo. Folders are created on demand by /audit-share Step 5 (when the user actually shares the first file to that repo). This avoids littering empty folders into repos the user may not actively use.

Initial sync offer:

Prompt the user:

"Run /audit-share now to review your existing personal knowledge for sharing? This is the cold-start sweep — without it, the feature is enabled but nothing is shared yet (every audit-share run is opt-in per item). (Y/n, default y):"

If yes: invoke /audit-share inline as the next action. The user will see the audit-share batch summary and decide what to share. Setup's Step 8 (Confirm) runs after audit-share completes.

If no: continue to Step 8. Note in setup output: "Shared knowledge enabled but not yet populated. Run /audit-share anytime to do an initial sweep, or it'll surface candidates as they accumulate in your knowledge folder."

Step 7e: Self-Validation Audit (v2.15.2+)

After Step 7b's round-trip verification, run a coverage audit to catch any KT_* fields documented in bin/config.sh but missing from the user's written config. This is a defense-in-depth check against the wizard's own discipline failures — if Step 6's Advanced Options bundle silently skipped surfacing a key (e.g., the active_knowledge_surfacing gap that bit v2.15.1's first users), this step catches it before the user leaves /setup thinking everything is current.

Algorithm:

1. Enumerate known user-facing field names by reading ${ARIA_PLUGIN_ROOT}/bin/config.sh and extracting them from the parse lines. Each known field has the shape:

   KT_FIELDNAME=$(sed -n '/^---$/,/^---$/p' "$KT_CONFIG" | grep '^fieldname:' | sed 's/^fieldname: *//')
   

   Use grep -oE "grep '\\^[a-z_]+:'" "${ARIA_PLUGIN_ROOT}/bin/config.sh" | grep -oE '[a-z_]+' to extract the user-facing field names — those are the canonical list of fields the wizard should have covered.

2. For each known field, grep the just-written config ~/.claude/aria-knowledge.local.md for ^{fieldname}:. If the grep returns zero hits, add to a MISSING_FIELDS list.

3. If MISSING_FIELDS is non-empty:

   • Output: Self-validation found {N} known field(s) missing from your config: {field1}, {field2}, ...
   • For each missing field, look up its default value by reading the matching KT_FIELDNAME=${KT_FIELDNAME:-default} line in bin/config.sh. If no default is set, treat as empty.
   • Prompt: "Add all {N} missing fields with their defaults? (y/n/select): {field1}={default1}, {field2}={default2}, ..."
   • If user answers y: append each missing field as fieldname: default between the last column-1 hook-parsed field and the closing --- of the frontmatter. Re-run Step 7b's round-trip verification on the additions.
   • If user answers n: emit a one-liner to the setup output: "Self-validation skipped: {N} field(s) missing ({list}). Run /audit-config later to surface them again, or hand-add to ~/.claude/aria-knowledge.local.md." Do not block setup.
   • If user answers select: walk per-field, prompting Add {fieldname}: {default}? (y/n) for each. Aggregate decisions; apply approved fields atomically.

4. If MISSING_FIELDS is empty: print Self-validation passed: all {N} known fields present in config.

Why this exists (v2.15.2 Origin): the [NEW] detection in Step 6's Advanced Options was specced to surface new-since-last-setup keys, but Step 6 is a soft instruction to Claude — it's not hook-enforced, so a fast or quiet /setup run can silently skip the detection. Step 7e is a final verification gate that runs against the canonical config.sh source of truth, surfacing any gap regardless of how the wizard got there. Pairs with /audit-config's missing-known-fields cascade check (Step 3b) as the audit-cadence safety net.

Step 8: Confirm

Output a summary:

Setup complete for ARIA v[INSTALLED_VERSION].
- Knowledge folder: [path]
- Knowledge audit: every [N] days
- Config audit: every [N] days
- Update check: every [N] days
- Insight capture: [enabled/disabled]
- Auto-capture on compaction: [enabled/disabled]
- Ticketing plugins: [N mappings configured | not configured (empty — change anytime by re-running /setup; the advanced-options bundle always shows the current value)]
- Shared knowledge: [enabled (author_tag: {tag}) | disabled (opt-in via re-run /setup)]
- Files added: [N]
- Files updated: [N]
- Files kept (user version): [N]

Two habits that make ARIA most effective:
- Run /extract before ending sessions — captures knowledge while the full conversation is in context
- Respond to "Knowledge audit due" prompts — promotes pending items so /context can surface them later
Everything else runs automatically via hooks.