@open-agent-toolkit/cli 0.0.18 → 0.0.20

package/assets/docs/cli-utilities/config-and-local-state.md

@@ -54,6 +54,18 @@ Archive lifecycle settings live here as shared repo config:
 - `archive.s3SyncOnComplete`
 - `archive.summaryExportPath`
 
+Tool-pack installation state also lives here as shared repo config:
+
+- `tools.core`
+- `tools.docs`
+- `tools.ideas`
+- `tools.project-management`
+- `tools.research`
+- `tools.utility`
+- `tools.workflows`
+
+Use `oat config get tools.<pack>` when you need an explicit installed-capability signal for workflows or troubleshooting.
+
 When archive settings are configured, completion uploads dated archive snapshots to S3 and exports dated summary snapshots into the configured summary reference directory.
 
 Use these reference pages for file ownership and schema details:

package/assets/docs/cli-utilities/configuration.md

@@ -18,12 +18,12 @@ For the deep file-by-file reference, see:
 
 ## The four config surfaces
 
-| Surface              | File                     | Typical contents                                                                                                 | Primary CLI surface                        |
-| -------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------- | ------------------------------------------ |
-| Shared repo config   | `.oat/config.json`       | Repo-wide non-sync settings such as `projects.root`, `git.defaultBranch`, `documentation.*`, and `archive.*`     | `oat config get/set/list/describe`         |
-| Repo-local config    | `.oat/config.local.json` | Per-developer state for this checkout, such as `activeProject`, `lastPausedProject`, and repo-local `activeIdea` | `oat config get/set/list/describe`         |
-| User config          | `~/.oat/config.json`     | User-level state such as global `activeIdea` fallback                                                            | `oat config describe`                      |
-| Provider sync config | `.oat/sync/config.json`  | Provider enablement and sync strategy settings                                                                   | `oat providers set`, `oat config describe` |
+| Surface              | File                     | Typical contents                                                                                                        | Primary CLI surface                        |
+| -------------------- | ------------------------ | ----------------------------------------------------------------------------------------------------------------------- | ------------------------------------------ |
+| Shared repo config   | `.oat/config.json`       | Repo-wide non-sync settings such as `projects.root`, `git.defaultBranch`, `documentation.*`, `archive.*`, and `tools.*` | `oat config get/set/list/describe`         |
+| Repo-local config    | `.oat/config.local.json` | Per-developer state for this checkout, such as `activeProject`, `lastPausedProject`, and repo-local `activeIdea`        | `oat config get/set/list/describe`         |
+| User config          | `~/.oat/config.json`     | User-level state such as global `activeIdea` fallback                                                                   | `oat config describe`                      |
+| Provider sync config | `.oat/sync/config.json`  | Provider enablement and sync strategy settings                                                                          | `oat providers set`, `oat config describe` |
 
 The main split is:
 
@@ -64,6 +64,16 @@ Common keys in `.oat/config.json`:
 - `archive.s3Uri` — base S3 archive prefix
 - `archive.s3SyncOnComplete` — upload archived projects to S3 during completion
 - `archive.summaryExportPath` — export `summary.md` into a durable tracked directory during completion
+- `tools.<pack>` — whether a bundled tool pack is currently installed in the repo or user scopes after lifecycle reconciliation
+
+Tool-pack state example:
+
+```bash
+oat config get tools.project-management
+oat config set tools.project-management true
+```
+
+The `tools.*` keys are primarily maintained by `oat tools install`, `oat tools update`, and `oat tools remove`, but they are intentionally visible through `oat config` so workflows and operators can inspect or override pack-state signals when needed.
 
 Archive example:
 

package/assets/docs/cli-utilities/tool-packs.md

@@ -74,6 +74,7 @@ Key behavior:
 - Same pack selection and install flow as `oat init tools`
 - Pack-oriented install subcommands: `core`, `docs`, `ideas`, `workflows`, `utility`, `project-management`, `research`
 - Tracks installed vs bundled skill versions and reports outdated skills
+- Records installed pack state in shared repo config as `tools.<pack>: true` so other OAT workflows can detect installed capabilities without relying on filesystem heuristics
 - Interactive runs can prompt to update selected outdated skills
 - Auto-sync runs automatically after successful install (provider views are updated)
 - Use `--no-sync` to skip auto-sync
@@ -89,6 +90,7 @@ Key behavior:
 - Accepts a tool name, `--pack <pack>`, or `--all` (mutually exclusive)
 - Compares installed versions against bundled versions and copies updated assets
 - For `--pack <pack>` and `--all`, an already-installed pack is reconciled to include newly added bundled skills or agents in that same scope
+- For `--pack <pack>` and `--all`, shared repo config is also reconciled from an installed-pack scan so `tools.*` reflects what is actually available and stale `true` flags are cleared
 - Dry-run mode with `--dry-run`; auto-sync after mutations by default
 - Use `--no-sync` to skip auto-sync
 - Reports tools that are already current, newer than bundled, or not bundled (custom)
@@ -103,9 +105,20 @@ Key behavior:
 
 - Accepts a tool name, `--pack <pack>`, or `--all` (mutually exclusive)
 - Removes skill directories and agent `.md` files from canonical locations
+- For `--pack <pack>` and `--all`, shared repo config is rewritten from a post-removal scan so `tools.<pack>` becomes `false` when a pack is no longer installed in any scope
 - Dry-run mode with `--dry-run`; auto-sync after mutations by default
 - Use `--no-sync` to skip auto-sync
 
+## Shared config signal: `tools.*`
+
+Tool-pack lifecycle commands now persist pack availability in shared repo config under `.oat/config.json`.
+
+- `oat tools install <pack>` writes `tools.<pack>: true`
+- `oat tools update --pack <pack>` and `oat tools update --all` rebuild the full `tools` map from installed-pack scans
+- `oat tools remove --pack <pack>` and `oat tools remove --all` rebuild the same map after removals
+
+This matters because other workflows can now check `oat config get tools.<pack>` instead of inferring capabilities from directory existence alone. For example, `oat-project-document` checks `tools.project-management` before auto-running repo-reference refresh work.
+
 ## Core pack
 
 The `core` pack contains foundational diagnostic and documentation skills:

package/assets/docs/workflows/projects/lifecycle.md

@@ -18,7 +18,7 @@ OAT lifecycle order:
 7. Summary (`oat-project-summary`) — generates `summary.md` as institutional memory; `oat-project-pr-final` and `oat-project-complete` auto-refresh it when missing or stale
 8. PR (`oat-project-pr-progress` / `oat-project-pr-final`) — sets `pr_open` status
 9. Revision loop (`oat-project-revise`) — optional; accepts post-PR feedback
-10. Documentation sync (`oat-project-document`) — optional; reads project artifacts to identify docs needing updates
+10. Documentation sync (`oat-project-document`) — optional; reads project artifacts to identify docs needing updates, checks `tools.project-management`, and auto-runs `oat-pjm-update-repo-reference` before scanning docs when the project-management pack is installed
 11. Complete (`oat-project-complete`)
 
 **Shortcut:** `oat-project-next` reads project state and invokes the correct next skill automatically — use it instead of remembering which skill comes next. Complements `oat-project-progress` (which is read-only diagnostic).
@@ -49,7 +49,7 @@ flowchart LR
 After implementation and final review pass:
 
 1. **Summary** (`oat-project-summary`) — generates `summary.md` as institutional memory from project artifacts; PR-final and completion will auto-refresh it if you have not already run it or if it is stale
-2. **Documentation** (`oat-project-document`) — optional sync of project docs
+2. **Documentation** (`oat-project-document`) — optional sync of project docs; now uses the shared `tools.project-management` config signal to decide whether repo-reference refresh should run before docs analysis
 3. **PR** (`oat-project-pr-final`) — creates PR description (auto-refreshes `summary.md` first when needed, then uses it as source), sets `oat_phase_status: pr_open`, and tracks actual PR existence with `oat_pr_status` / `oat_pr_url`
 4. **Revision loop** (`oat-project-revise`) — accepts post-PR feedback:
    - Inline feedback creates `p-revN` revision phases with `prevN-tNN` task IDs

package/assets/public-package-versions.json

@@ -1,6 +1,6 @@
 {
-  "cli": "0.0.18",
-  "docs-config": "0.0.18",
-  "docs-theme": "0.0.18",
-  "docs-transforms": "0.0.18"
+  "cli": "0.0.20",
+  "docs-config": "0.0.20",
+  "docs-theme": "0.0.20",
+  "docs-transforms": "0.0.20"
 }

package/assets/skills/oat-project-complete/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: oat-project-complete
-version: 1.3.5
+version: 1.3.6
 description: Use when all implementation work is finished and the project is ready to close. Marks the OAT project lifecycle as complete.
 disable-model-invocation: true
 user-invocable: true
@@ -343,7 +343,7 @@ echo "Project archived to $ARCHIVE_PATH"
 
 - Always archive locally first. The local archive is the authoritative completion artifact even when remote sync is also configured.
 - If `archive.summaryExportPath` is configured and `summary.md` exists after archive, copy it to `{repoRoot}/{archive.summaryExportPath}/YYYYMMDD-{PROJECT_NAME}.md`.
-- If `archive.s3SyncOnComplete=true` and `archive.s3Uri` is configured, sync the archived project to `{archive.s3Uri}/{repo-slug}/{PROJECT_NAME}/`.
+- If `archive.s3SyncOnComplete=true` and `archive.s3Uri` is configured, sync the archived project to `{archive.s3Uri}/{repo-slug}/{PROJECT_NAME}/`. The S3 sync excludes process artifacts (`reviews/*`, `pr/*`) — only core deliverables (discovery, spec, design, plan, implementation, summary, state) are uploaded. The CLI enforces this via `S3_ARCHIVE_SYNC_EXCLUDES` in `archive-utils.ts`.
 - If AWS CLI is missing or unusable for that S3 sync, warn and continue. Completion must not fail after the local archive succeeds.
 - If `archive.s3SyncOnComplete` is false or `archive.s3Uri` is unset, skip remote sync without prompting.
 

package/assets/skills/oat-project-document/SKILL.md

@@ -1,11 +1,11 @@
 ---
 name: oat-project-document
-version: 1.0.1
+version: 1.2.0
 description: Run when implementation is complete and documentation needs updating. Analyzes project artifacts to produce documentation update recommendations, then applies approved changes before project completion.
 argument-hint: '[project-path] [--auto]'
 disable-model-invocation: true
 user-invocable: true
-allowed-tools: Read, Write, Edit, Bash(git:*), Glob, Grep, AskUserQuestion
+allowed-tools: Read, Write, Edit, Bash(git:*), Glob, Grep, AskUserQuestion, Skill
 ---
 
 # Project Documentation Sync
@@ -140,7 +140,24 @@ Glob: **/docusaurus.config.{js,ts}
 
 Store resolved values for use in later steps. Do not write auto-detected values to config.
 
-### Step 1: Read Project Artifacts
+### Step 1: Check for PJM Infrastructure
+
+Check whether the project-management tool pack is installed by reading config:
+
+```bash
+PJM_INSTALLED=$(oat config get tools.project-management 2>/dev/null || echo "false")
+```
+
+**If `PJM_INSTALLED` is `true`:**
+
+- Invoke `oat-pjm-update-repo-reference` automatically before proceeding.
+- Do not ask whether to run the repo reference update during project-document.
+- **If invocation succeeds:** Log that repo reference docs were refreshed and continue to Step 2. The reference surfaces will already be current when the documentation scan reads them in Step 4a.4.
+- **If invocation fails:** Warn the user that the repo reference update failed, but continue with the documentation sync — a PJM failure should not block documentation updates.
+
+**If `PJM_INSTALLED` is not `true`:** Skip silently and proceed to Step 2.
+
+### Step 2: Read Project Artifacts
 
 Read all available project artifacts to build an understanding of what was built.
 
@@ -171,14 +188,14 @@ While reading artifacts, collect all source file paths mentioned in:
 - Implementation.md `**Files changed:**` entries
 - Design component interfaces and data models
 
-These will be verified against actual code in Step 2.
+These will be verified against actual code in Step 3.
 
 **Handle missing artifacts gracefully:**
 
 - Quick-mode projects may lack spec.md and design.md — extract what's available
 - If only plan.md exists (no implementation.md), the project may not have started implementation yet — still proceed, but note that documentation recommendations will be based on planned work rather than verified implementation
 
-### Step 2: Verify Against Code
+### Step 3: Verify Against Code
 
 Read source files referenced in artifacts to confirm what actually shipped.
 
@@ -201,11 +218,11 @@ Read source files referenced in artifacts to confirm what actually shipped.
 - If artifacts reference many files (>20), prioritize: new files first, then modified files with the most changes
 - Read file contents, not just check existence — the skill needs to understand what the code does to make good documentation recommendations
 
-### Step 3: Discover Documentation Surfaces
+### Step 4: Discover Documentation Surfaces
 
 Scan the repository for all documentation and instruction surfaces.
 
-**3a. Documentation surfaces (primary — thorough analysis):**
+**4a. Documentation surfaces (primary — thorough analysis):**
 
 1. **Docs directory** (if `$DOCS_ROOT` is set):
    - Read the docs tooling config (e.g., `$DOCS_CONFIG`) to understand nav structure
@@ -224,7 +241,7 @@ Scan the repository for all documentation and instruction surfaces.
    - Check `.oat/repo/reference/` directory
    - Read: `current-state.md`, `backlog/index.md`, `backlog/completed.md`, `roadmap.md`, `decision-record.md`, and relevant `backlog/items/*.md` files as needed (whichever exist)
 
-**3b. Instruction surfaces (secondary — strong signals only):**
+**4b. Instruction surfaces (secondary — strong signals only):**
 
 1. **Root AGENTS.md / CLAUDE.md:**
    - Always check — read current content
@@ -242,18 +259,18 @@ Scan the repository for all documentation and instruction surfaces.
      - Gemini: `.gemini/rules/`
    - Read existing rules files that may need updating
 
-**Store surface inventory** for use in Step 4. For each surface, record:
+**Store surface inventory** for use in Step 5. For each surface, record:
 
 - File path (existing or potential)
 - Surface type (docs | readme | reference | agents | provider-rules)
 - Current content summary (for existing files)
 - Whether it's in a directory affected by the project
 
-### Step 4: Assess Documentation Delta
+### Step 5: Assess Documentation Delta
 
-Compare "what was built" (from Steps 1-2) against "what's documented" (from Step 3) to produce recommendations.
+Compare "what was built" (from Steps 2-3) against "what's documented" (from Step 4) to produce recommendations.
 
-**4a. Documentation surface assessment:**
+**5a. Documentation surface assessment:**
 
 For each documentation surface relevant to the project, determine one of:
 
@@ -274,7 +291,7 @@ For each documentation surface relevant to the project, determine one of:
 
 - **No change:** Surface is already accurate — skip from delta plan.
 
-**4b. Instruction surface assessment (strong signals only):**
+**5b. Instruction surface assessment (strong signals only):**
 
 Only recommend instruction changes when there is a clear trigger:
 
@@ -288,7 +305,7 @@ Only recommend instruction changes when there is a clear trigger:
 
 If no strong signal is present for an instruction surface, skip it.
 
-**4c. Per recommendation, capture:**
+**5c. Per recommendation, capture:**
 
 ```
 - Target: {file path — existing or proposed}
@@ -298,11 +315,11 @@ If no strong signal is present for an instruction surface, skip it.
 - Content guidance: {specific content to add or outline for new files}
 ```
 
-### Step 5: Present Delta Plan
+### Step 6: Present Delta Plan
 
 Format and present the recommendations for user approval.
 
-**5a. Format output:**
+**6a. Format output:**
 
 ```
 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
@@ -326,13 +343,13 @@ Format and present the recommendations for user approval.
    Evidence: {reference}
 ```
 
-**5b. Handle edge cases:**
+**6b. Handle edge cases:**
 
-- If `$AUTO_MODE` is true: skip to Step 6 (apply all recommendations)
+- If `$AUTO_MODE` is true: skip to Step 7 (apply all recommendations)
 - If no recommendations found: report "No documentation updates identified for this project.", set `oat_docs_updated: complete` in state.md, and exit
 - If only instruction recommendations (no docs): still present, but note the documentation-first priority
 
-**5c. Interactive approval:**
+**6c. Interactive approval:**
 
 ```
 Approve recommendations?
@@ -345,9 +362,9 @@ Approve recommendations?
 - **Individual:** present each recommendation one at a time with approve/reject
 - **Skip:** set `oat_docs_updated: skipped` and `oat_project_state_updated: "{ISO 8601 UTC timestamp}"` in `$PROJECT_PATH/state.md` frontmatter, commit the state change, and exit without applying documentation changes
 
-Track which recommendations were approved for Step 6.
+Track which recommendations were approved for Step 7.
 
-### Step 6: Apply Approved Changes
+### Step 7: Apply Approved Changes
 
 Execute the approved documentation updates.
 
@@ -382,36 +399,36 @@ If `$DOCS_CONFIG` exists and new files were created in the docs directory:
 - Track a `$ALL_SUCCEEDED` flag (default: true). If any file write fails, set `$ALL_SUCCEEDED` to false, log the error, and continue with remaining recommendations
 - At the end, report any failures with the specific files that could not be written
 
-### Step 7: Commit and Update State
+### Step 8: Commit and Update State
 
-**7a. Stage and commit documentation changes:**
+**8a. Stage and commit documentation changes:**
 
 ```bash
 git add {list of changed/created documentation files}
 git diff --cached --quiet || git commit -m "docs({project-name}): update documentation from project artifacts"
 ```
 
-Only stage files that were actually changed or created in Step 6. Do not use `git add -A`.
+Only stage files that were actually changed or created in Step 7. Do not use `git add -A`.
 
-**7b. Update project state:**
+**8b. Update project state:**
 
 Update `$PROJECT_PATH/state.md` frontmatter based on apply outcome:
 
 - If `$ALL_SUCCEEDED` is true: set `oat_docs_updated: complete` and `oat_project_state_updated: "{ISO 8601 UTC timestamp}"`
-- If `$ALL_SUCCEEDED` is false: do **not** set `oat_docs_updated: complete` — leave the field as `null` so the skill can be re-run. Still set `oat_project_state_updated: "{ISO 8601 UTC timestamp}"`. Surface the failures clearly in the summary report (Step 7d) so the user knows which updates failed and why.
+- If `$ALL_SUCCEEDED` is false: do **not** set `oat_docs_updated: complete` — leave the field as `null` so the skill can be re-run. Still set `oat_project_state_updated: "{ISO 8601 UTC timestamp}"`. Surface the failures clearly in the summary report (Step 8d) so the user knows which updates failed and why.
 
 ```bash
 git add "$PROJECT_PATH/state.md"
 git diff --cached --quiet || git commit -m "chore({project-name}): mark docs updated"
 ```
 
-**7c. Handle edge cases:**
+**8c. Handle edge cases:**
 
-- If user explicitly skipped (chose [S]kip in Step 5): `oat_docs_updated` was already set to `skipped` in Step 5. No further state update needed here.
+- If user explicitly skipped (chose [S]kip in Step 6): `oat_docs_updated` was already set to `skipped` in Step 6. No further state update needed here.
 - If no recommendations were found: set `oat_docs_updated: complete` (nothing to do is still "done").
 - If `--auto` mode: apply all, commit, set state — no user interaction.
 
-**7d. Report summary:**
+**8d. Report summary:**
 
 If `$ALL_SUCCEEDED` is true:
 

package/dist/commands/config/index.d.ts.map

@@ -1 +1 @@
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package/dist/commands/config/index.js

@@ -18,6 +18,13 @@ const KEY_ORDER = [
     'documentation.requireForProjectCompletion',
     'git.defaultBranch',
     'projects.root',
+    'tools.core',
+    'tools.docs',
+    'tools.ideas',
+    'tools.project-management',
+    'tools.research',
+    'tools.utility',
+    'tools.workflows',
     'worktrees.root',
 ];
 const CONFIG_CATALOG = [
@@ -142,6 +149,83 @@ const CONFIG_CATALOG = [
         owningCommand: 'oat config set archive.summaryExportPath <value>',
         description: 'Repository-relative directory where completion copies project summaries for durable tracked reference.',
     },
+    {
+        key: 'tools.core',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'boolean',
+        defaultValue: 'false',
+        mutability: 'read/write',
+        owningCommand: 'oat tools install / oat tools update',
+        description: 'Whether the core tool pack is installed.',
+    },
+    {
+        key: 'tools.docs',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'boolean',
+        defaultValue: 'false',
+        mutability: 'read/write',
+        owningCommand: 'oat tools install / oat tools update',
+        description: 'Whether the docs tool pack is installed.',
+    },
+    {
+        key: 'tools.ideas',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'boolean',
+        defaultValue: 'false',
+        mutability: 'read/write',
+        owningCommand: 'oat tools install / oat tools update',
+        description: 'Whether the ideas tool pack is installed.',
+    },
+    {
+        key: 'tools.project-management',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'boolean',
+        defaultValue: 'false',
+        mutability: 'read/write',
+        owningCommand: 'oat tools install / oat tools update',
+        description: 'Whether the project-management tool pack is installed.',
+    },
+    {
+        key: 'tools.research',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'boolean',
+        defaultValue: 'false',
+        mutability: 'read/write',
+        owningCommand: 'oat tools install / oat tools update',
+        description: 'Whether the research tool pack is installed.',
+    },
+    {
+        key: 'tools.utility',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'boolean',
+        defaultValue: 'false',
+        mutability: 'read/write',
+        owningCommand: 'oat tools install / oat tools update',
+        description: 'Whether the utility tool pack is installed.',
+    },
+    {
+        key: 'tools.workflows',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'boolean',
+        defaultValue: 'false',
+        mutability: 'read/write',
+        owningCommand: 'oat tools install / oat tools update',
+        description: 'Whether the workflows tool pack is installed.',
+    },
     {
         key: 'activeProject',
         group: 'Repo Local (.oat/config.local.json)',
@@ -316,6 +400,16 @@ async function getConfigValue(repoRoot, key, dependencies) {
             source: archive ? 'config.json' : 'default',
         };
     }
+    if (key.startsWith('tools.')) {
+        const config = await dependencies.readOatConfig(repoRoot);
+        const packName = key.slice('tools.'.length);
+        const tools = config.tools ?? {};
+        return {
+            key,
+            value: String(tools[packName] ?? false),
+            source: config.tools ? 'config.json' : 'default',
+        };
+    }
     if (key === 'git.defaultBranch') {
         const config = await dependencies.readOatConfig(repoRoot);
         return {
@@ -437,6 +531,20 @@ async function setConfigValue(repoRoot, key, rawValue, dependencies) {
             source: 'config.json',
         };
     }
+    if (key.startsWith('tools.')) {
+        const packName = key.slice('tools.'.length);
+        const tools = { ...config.tools };
+        tools[packName] = rawValue.trim().toLowerCase() === 'true';
+        await dependencies.writeOatConfig(repoRoot, {
+            ...config,
+            tools,
+        });
+        return {
+            key,
+            value: String(tools[packName] ?? false),
+            source: 'config.json',
+        };
+    }
     if (key === 'git.defaultBranch') {
         const nextValue = rawValue.trim();
         if (!nextValue) {

package/dist/commands/init/tools/index.d.ts

@@ -35,6 +35,7 @@ interface InitToolsDependencies {
         action: string;
     }>;
     readOatConfig: (repoRoot: string) => Promise<OatConfig>;
+    writeOatConfig: (repoRoot: string, config: OatConfig) => Promise<void>;
     resolveLocalPaths: (config: OatConfig) => string[];
     upsertAgentsMdSection: (repoRoot: string, key: string, body: string) => Promise<UpsertSectionResult>;
     removeAgentsMdSection: (repoRoot: string, key: string) => Promise<boolean>;

package/dist/commands/init/tools/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/init/tools/index.ts"],"names":[],"mappings":"AAEA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAI9B,OAAO,EACL,KAAK,mBAAmB,EAGzB,MAAM,4BAA4B,CAAC;AACpC,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,aAAa,EAClB,KAAK,YAAY,EAGlB,MAAM,iCAAiC,CAAC;AAEzC,OAAO,EACL,KAAK,SAAS,EAIf,MAAM,oBAAoB,CAAC;AAG5B,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAGpC,OAAO,EAEL,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACvB,MAAM,qBAAqB,CAAC;AAE7B,OAAO,EAGL,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACvB,MAAM,qBAAqB,CAAC;AAE7B,OAAO,EAEL,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACxB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EAEL,KAAK,+BAA+B,EACpC,KAAK,8BAA8B,EACpC,MAAM,iDAAiD,CAAC;AAEzD,OAAO,EAEL,KAAK,sBAAsB,EAC3B,KAAK,qBAAqB,EAE3B,MAAM,6BAA6B,CAAC;AAErC,OAAO,EAEL,KAAK,qBAAqB,EAC1B,KAAK,oBAAoB,EAE1B,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EAEL,KAAK,uBAAuB,EAC5B,KAAK,sBAAsB,EAC5B,MAAM,+BAA+B,CAAC;AAEvC,KAAK,YAAY,GAAG,SAAS,GAAG,MAAM,CAAC;AACvC,MAAM,MAAM,QAAQ,GAChB,MAAM,GACN,OAAO,GACP,MAAM,GACN,WAAW,GACX,SAAS,GACT,oBAAoB,GACpB,UAAU,CAAC;AAEf,UAAU,qBAAqB;IAC7B,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,kBAAkB,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IACrD,gBAAgB,EAAE,CAAC,KAAK,EAAE,YAAY,EAAE,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC;IAC7E,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,mBAAmB,EAAE,CAAC,CAAC,SAAS,MAAM,EACpC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAC/B,GAAG,EAAE,aAAa,KACf,OAAO,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,CAAC;IACzB,eAAe,EAAE,CAAC,CAAC,SAAS,MAAM,EAChC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,YAAY,CAAC,CAAC,CAAC,EAAE,EAC1B,GAAG,EAAE,aAAa,KACf,OAAO,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;IACvB,WAAW,EAAE,CAAC,OAAO,EAAE,kBAAkB,KAAK,OAAO,CAAC,iBAAiB,CAAC,CAAC;IACzE,WAAW,EAAE,CAAC,OAAO,EAAE,kBAAkB,KAAK,OAAO,CAAC,iBAAiB,CAAC,CAAC;IACzE,YAAY,EAAE,CAAC,OAAO,EAAE,mBAAmB,KAAK,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC5E,gBAAgB,EAAE,CAChB,OAAO,EAAE,uBAAuB,KAC7B,OAAO,CAAC,sBAAsB,CAAC,CAAC;IACrC,cAAc,EAAE,CACd,OAAO,EAAE,qBAAqB,KAC3B,OAAO,CAAC,oBAAoB,CAAC,CAAC;IACnC,wBAAwB,EAAE,CACxB,OAAO,EAAE,+BAA+B,KACrC,OAAO,CAAC,8BAA8B,CAAC,CAAC;IAC7C,eAAe,EAAE,CACf,OAAO,EAAE,sBAAsB,KAC5B,OAAO,CAAC,qBAAqB,CAAC,CAAC;IACpC,iBAAiB,EAAE,CACjB,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,OAAO,KACX,OAAO,CAAC,QAAQ,GAAG,SAAS,GAAG,SAAS,CAAC,CAAC;IAC/C,aAAa,EAAE,CACb,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,MAAM,EAAE,KACZ,OAAO,CAAC;QAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QAAC,GAAG,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC,CAAC;IACjD,cAAc,EAAE,CACd,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAAE,KACjB,OAAO,CAAC;QAAE,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACjC,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,cAAc,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IACvE,iBAAiB,EAAE,CAAC,MAAM,EAAE,SAAS,KAAK,MAAM,EAAE,CAAC;IACnD,qBAAqB,EAAE,CACrB,QAAQ,EAAE,MAAM,EAChB,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,KACT,OAAO,CAAC,mBAAmB,CAAC,CAAC;IAClC,qBAAqB,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;CAC5E;AAsMD,UAAU,aAAa;IACrB,IAAI,EAAE,QAAQ,CAAC;IACf,KAAK,EAAE,YAAY,CAAC;CACrB;AAED,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,aAAa,EAAE,GAAG,MAAM,CAuCxE;AAED,wBAAsB,YAAY,CAChC,OAAO,EAAE,cAAc,EACvB,YAAY,EAAE,qBAAqB,GAClC,OAAO,CAAC,QAAQ,EAAE,CAAC,CA6PrB;AAED,wBAAsB,wBAAwB,CAC5C,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,QAAQ,EAAE,CAAC,CAErB;AAED,wBAAgB,sBAAsB,CACpC,SAAS,GAAE,OAAO,CAAC,qBAAqB,CAAM,GAC7C,OAAO,CAuBT"}

package/dist/commands/init/tools/index.js

@@ -6,7 +6,7 @@ import { addLocalPaths } from '../../local/manage.js';
 import { removeAgentsMdSection, upsertAgentsMdSection, } from '../../shared/agents-md.js';
 import { selectManyWithAbort, selectWithAbort, } from '../../shared/shared.prompts.js';
 import { readGlobalOptions } from '../../shared/shared.utils.js';
-import { readOatConfig, resolveLocalPaths, } from '../../../config/oat-config.js';
+import { readOatConfig, resolveLocalPaths, writeOatConfig, } from '../../../config/oat-config.js';
 import { resolveAssetsRoot } from '../../../fs/assets.js';
 import { resolveProjectRoot, resolveScopeRoot } from '../../../fs/paths.js';
 import { Command } from 'commander';
@@ -58,6 +58,7 @@ const DEFAULT_DEPENDENCIES = {
     addLocalPaths,
     applyGitignore,
     readOatConfig,
+    writeOatConfig,
     resolveLocalPaths,
     upsertAgentsMdSection,
     removeAgentsMdSection,
@@ -346,6 +347,12 @@ export async function runInitTools(context, dependencies) {
         if (!context.json && sectionResult.action !== 'no-change') {
             context.logger.info(`AGENTS.md tool packs section ${sectionResult.action}.`);
         }
+        const config = await dependencies.readOatConfig(projectRoot);
+        const tools = { ...config.tools };
+        for (const pack of selectedPacks) {
+            tools[pack] = true;
+        }
+        await dependencies.writeOatConfig(projectRoot, { ...config, tools });
         const hasUserScope = selectedPacks.some((pack) => packScopes[pack] === 'user');
         reportSuccess(context, selectedPacks, hasUserScope ? 'user' : 'project');
         process.exitCode = 0;

package/dist/commands/project/archive/archive-utils.d.ts

@@ -51,6 +51,11 @@ export interface ArchiveProjectOnCompletionResult {
     warnings: string[];
 }
 export declare const ARCHIVE_SNAPSHOT_METADATA_FILENAME = ".oat-archive-source.json";
+/**
+ * Directories excluded from S3 archive sync. These contain process artifacts
+ * (reviews, PR descriptions) rather than project deliverables.
+ */
+export declare const S3_ARCHIVE_SYNC_EXCLUDES: string[];
 export interface ArchiveSnapshotMetadata {
     projectName: string;
     snapshotName: string;

package/dist/commands/project/archive/archive-utils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"archive-utils.d.ts","sourceRoot":"","sources":["../../../../src/commands/project/archive/archive-utils.ts"],"names":[],"mappings":"AAMA,OAAO,EACL,aAAa,EACb,cAAc,EACd,SAAS,EACT,SAAS,EACT,UAAU,EACX,MAAM,QAAQ,CAAC;AAIhB,MAAM,MAAM,cAAc,GAAG;IAC3B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,MAAM,CAAC;CAChB,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG,CACzB,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,EAAE,EACd,OAAO,CAAC,EAAE;IAAE,GAAG,CAAC,EAAE,MAAM,CAAC;IAAC,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAA;CAAE,KAChD,OAAO,CAAC,cAAc,CAAC,CAAC;AAE7B,MAAM,WAAW,4BAA4B;IAC3C,IAAI,EAAE,YAAY,GAAG,MAAM,CAAC;IAC5B,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,cAAc,EAAE,OAAO,CAAC;CACzB;AAED,UAAU,iCAAiC;IACzC,QAAQ,CAAC,EAAE,YAAY,CAAC;IACxB,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;CACzB;AAED,MAAM,WAAW,2BAA2B;IAC1C,EAAE,EAAE,OAAO,CAAC;IACZ,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,iCAAiC;IAChD,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,MAAM,CAAC;IACrB,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,gBAAgB,EAAE,OAAO,CAAC;IAC1B,iBAAiB,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;CACnC;AAED,UAAU,sCAAuC,SAAQ,iCAAiC;IACxF,qBAAqB,CAAC,EAAE,OAAO,qBAAqB,CAAC;IACrD,QAAQ,CAAC,EAAE,YAAY,CAAC;IACxB,WAAW,CAAC,EAAE,YAAY,CAAC;IAC3B,SAAS,CAAC,EAAE,OAAO,SAAS,CAAC;IAC7B,aAAa,CAAC,EAAE,OAAO,aAAa,CAAC;IACrC,UAAU,CAAC,EAAE,CACX,MAAM,EAAE,MAAM,EACd,OAAO,EAAE;QAAE,SAAS,EAAE,IAAI,CAAC;QAAC,KAAK,EAAE,IAAI,CAAA;KAAE,KACtC,OAAO,CAAC,IAAI,CAAC,CAAC;IACnB,cAAc,CAAC,EAAE,OAAO,cAAc,CAAC;IACvC,SAAS,CAAC,EAAE,OAAO,SAAS,CAAC;IAC7B,UAAU,CAAC,EAAE,OAAO,UAAU,CAAC;IAC/B,SAAS,CAAC,EAAE,MAAM,MAAM,CAAC;CAC1B;AAED,MAAM,WAAW,gCAAgC;IAC/C,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,iBAAiB,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,eAAO,MAAM,kCAAkC,6BAA6B,CAAC;AAE7E;;;GAGG;AACH,eAAO,MAAM,wBAAwB,UAAwB,CAAC;AAE9D,MAAM,WAAW,uBAAuB;IACtC,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,MAAM,CAAC;CACtB;AA8BD,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,MAAM,CAE7E;AAED,wBAAgB,wBAAwB,CACtC,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,GACjB,MAAM,CAER;AAmBD,wBAAgB,wBAAwB,CACtC,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB,MAAM,CAER;AAED,wBAAgB,wBAAwB,CAAC,YAAY,EAAE,MAAM,GAAG;IAC9D,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,MAAM,CAAC;IACrB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;CAC1B,CA4BA;AAED,wBAAgB,8BAA8B,CAC5C,YAAY,EAAE,MAAM,EACpB,WAAW,EAAE,MAAM,GAClB,MAAM,CAIR;AAqJD,wBAAsB,0BAA0B,CAC9C,OAAO,EAAE,iCAAiC,EAC1C,YAAY,GAAE,sCAA2C,GACxD,OAAO,CAAC,gCAAgC,CAAC,CAwG3C;AAED,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,4BAA4B,EACrC,YAAY,GAAE,iCAAsC,GACnD,OAAO,CAAC,2BAA2B,CAAC,CA0CtC"}

package/dist/commands/project/archive/archive-utils.js

@@ -6,6 +6,11 @@ import { CliError } from '../../../errors/cli-error.js';
 import { copyDirectory, copySingleFile, dirExists, ensureDir, fileExists, } from '../../../fs/io.js';
 const execFileAsync = promisify(execFileCallback);
 export const ARCHIVE_SNAPSHOT_METADATA_FILENAME = '.oat-archive-source.json';
+/**
+ * Directories excluded from S3 archive sync. These contain process artifacts
+ * (reviews, PR descriptions) rather than project deliverables.
+ */
+export const S3_ARCHIVE_SYNC_EXCLUDES = ['reviews/*', 'pr/*'];
 function normalizeS3Uri(s3Uri) {
     return s3Uri.trim().replace(/\/+$/, '');
 }
@@ -215,7 +220,11 @@ export async function archiveProjectOnCompletion(options, dependencies = {}) {
         if (access.ok) {
             s3Path = buildProjectArchiveS3Uri(options.s3Uri, options.repoRoot, snapshotName);
             try {
-                await execFile('aws', ['s3', 'sync', archivePath, s3Path], {
+                const syncArgs = ['s3', 'sync', archivePath, s3Path];
+                for (const pattern of S3_ARCHIVE_SYNC_EXCLUDES) {
+                    syncArgs.push('--exclude', pattern);
+                }
+                await execFile('aws', syncArgs, {
                     cwd: options.repoRoot,
                     env: dependencies.env ?? process.env,
                 });

package/dist/commands/project/archive/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/project/archive/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAY,EAAE,EAAE,MAAM,kBAAkB,CAAC;AAIhD,OAAO,EAAE,mBAAmB,EAAE,KAAK,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAGhF,OAAO,EAAE,KAAK,SAAS,EAAiB,MAAM,oBAAoB,CAAC;AAGnE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAEL,wBAAwB,EACxB,qBAAqB,EACrB,qBAAqB,EACrB,KAAK,YAAY,EAEjB,8BAA8B,EAC/B,MAAM,iBAAiB,CAAC;AASzB,MAAM,WAAW,iCAAiC;IAChD,mBAAmB,EAAE,CACnB,OAAO,EAAE,UAAU,CAAC,OAAO,mBAAmB,CAAC,CAAC,CAAC,CAAC,KAC/C,cAAc,CAAC;IACpB,kBAAkB,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IACrD,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,mBAAmB,EAAE,CACnB,QAAQ,EAAE,MAAM,EAChB,GAAG,EAAE,MAAM,CAAC,UAAU,KACnB,OAAO,CAAC,MAAM,CAAC,CAAC;IACrB,qBAAqB,EAAE,OAAO,qBAAqB,CAAC;IACpD,qBAAqB,EAAE,OAAO,qBAAqB,CAAC;IACpD,wBAAwB,EAAE,OAAO,wBAAwB,CAAC;IAC1D,8BAA8B,EAAE,OAAO,8BAA8B,CAAC;IACtE,QAAQ,EAAE,YAAY,CAAC;IACvB,eAAe,EAAE,OAAO,EAAE,CAAC;IAC3B,UAAU,EAAE,MAAM,CAAC,UAAU,CAAC;CAC/B;AAoLD,wBAAgB,2BAA2B,CACzC,SAAS,GAAE,OAAO,CAAC,iCAAiC,CAAM,GACzD,OAAO,CAuKT"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/project/archive/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAY,EAAE,EAAE,MAAM,kBAAkB,CAAC;AAIhD,OAAO,EAAE,mBAAmB,EAAE,KAAK,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAGhF,OAAO,EAAE,KAAK,SAAS,EAAiB,MAAM,oBAAoB,CAAC;AAGnE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAGL,wBAAwB,EACxB,qBAAqB,EACrB,qBAAqB,EACrB,KAAK,YAAY,EAEjB,8BAA8B,EAC/B,MAAM,iBAAiB,CAAC;AASzB,MAAM,WAAW,iCAAiC;IAChD,mBAAmB,EAAE,CACnB,OAAO,EAAE,UAAU,CAAC,OAAO,mBAAmB,CAAC,CAAC,CAAC,CAAC,KAC/C,cAAc,CAAC;IACpB,kBAAkB,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IACrD,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,mBAAmB,EAAE,CACnB,QAAQ,EAAE,MAAM,EAChB,GAAG,EAAE,MAAM,CAAC,UAAU,KACnB,OAAO,CAAC,MAAM,CAAC,CAAC;IACrB,qBAAqB,EAAE,OAAO,qBAAqB,CAAC;IACpD,qBAAqB,EAAE,OAAO,qBAAqB,CAAC;IACpD,wBAAwB,EAAE,OAAO,wBAAwB,CAAC;IAC1D,8BAA8B,EAAE,OAAO,8BAA8B,CAAC;IACtE,QAAQ,EAAE,YAAY,CAAC;IACvB,eAAe,EAAE,OAAO,EAAE,CAAC;IAC3B,UAAU,EAAE,MAAM,CAAC,UAAU,CAAC;CAC/B;AAwLD,wBAAgB,2BAA2B,CACzC,SAAS,GAAE,OAAO,CAAC,iCAAiC,CAAM,GACzD,OAAO,CAuKT"}

package/dist/commands/project/archive/index.js

@@ -9,7 +9,7 @@ import { readOatConfig } from '../../../config/oat-config.js';
 import { CliError } from '../../../errors/cli-error.js';
 import { resolveProjectRoot } from '../../../fs/paths.js';
 import { Command } from 'commander';
-import { ARCHIVE_SNAPSHOT_METADATA_FILENAME, buildProjectArchiveS3Uri, buildRepoArchiveS3Uri, ensureS3ArchiveAccess, parseArchiveSnapshotName, resolveLocalArchiveProjectPath, } from './archive-utils.js';
+import { ARCHIVE_SNAPSHOT_METADATA_FILENAME, S3_ARCHIVE_SYNC_EXCLUDES, buildProjectArchiveS3Uri, buildRepoArchiveS3Uri, ensureS3ArchiveAccess, parseArchiveSnapshotName, resolveLocalArchiveProjectPath, } from './archive-utils.js';
 const execFileAsync = promisify(execFileCallback);
 function defaultDependencies() {
     return {
@@ -31,6 +31,9 @@ function resolveLocalArchiveRoot(projectsRoot) {
 }
 function buildArchiveSyncArgs(source, target, options) {
     const args = ['s3', 'sync', source, target];
+    for (const pattern of S3_ARCHIVE_SYNC_EXCLUDES) {
+        args.push('--exclude', pattern);
+    }
     if (options.dryRun) {
         args.push('--dryrun');
     }

package/dist/commands/providers/inspect/inspect.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"inspect.d.ts","sourceRoot":"","sources":["../../../../src/commands/providers/inspect/inspect.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAGV,4BAA4B,EAC7B,MAAM,qCAAqC,CAAC;AAmB7C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA+KpC,wBAAgB,6BAA6B,CAC3C,SAAS,GAAE,OAAO,CAAC,4BAA4B,CAAM,GACpD,OAAO,CAiBT"}
+{"version":3,"file":"inspect.d.ts","sourceRoot":"","sources":["../../../../src/commands/providers/inspect/inspect.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAGV,4BAA4B,EAC7B,MAAM,qCAAqC,CAAC;AAmB7C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAuLpC,wBAAgB,6BAA6B,CAC3C,SAAS,GAAE,OAAO,CAAC,4BAA4B,CAAM,GACpD,OAAO,CAiBT"}

package/dist/commands/providers/inspect/inspect.js

@@ -71,6 +71,9 @@ async function collectInspectResult(providerName, context, dependencies) {
                 drifted: 0,
                 missing: 0,
             };
+            const copyTransform = mapping.transformCanonical
+                ? { transformCanonical: mapping.transformCanonical }
+                : undefined;
             for (const entry of manifest.entries) {
                 if (entry.provider !== adapter.name) {
                     continue;
@@ -79,7 +82,7 @@ async function collectInspectResult(providerName, context, dependencies) {
                     continue;
                 }
                 state.managed += 1;
-                const report = await dependencies.detectDrift(entry, scopeRoot.root);
+                const report = await dependencies.detectDrift(entry, scopeRoot.root, copyTransform);
                 if (report.state.status === 'in_sync') {
                     state.inSync += 1;
                     continue;

package/dist/commands/providers/list/list.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../../../src/commands/providers/list/list.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAGV,yBAAyB,EAC1B,MAAM,qCAAqC,CAAC;AAe7C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAsLpC,wBAAgB,0BAA0B,CACxC,SAAS,GAAE,OAAO,CAAC,yBAAyB,CAAM,GACjD,OAAO,CAcT"}
+{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../../../src/commands/providers/list/list.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAGV,yBAAyB,EAC1B,MAAM,qCAAqC,CAAC;AAmB7C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAwMpC,wBAAgB,0BAA0B,CACxC,SAAS,GAAE,OAAO,CAAC,yBAAyB,CAAM,GACjD,OAAO,CAcT"}

package/dist/commands/providers/list/list.js

@@ -2,7 +2,7 @@ import { join } from 'node:path';
 import { buildCommandContext } from '../../../app/command-context.js';
 import { readGlobalOptions, resolveConcreteScopes, } from '../../shared/shared.utils.js';
 import { detectDrift } from '../../../drift/index.js';
-import { resolveProjectRoot, resolveScopeRoot } from '../../../fs/paths.js';
+import { normalizeToPosixPath, resolveProjectRoot, resolveScopeRoot, } from '../../../fs/paths.js';
 import { loadManifest } from '../../../manifest/index.js';
 import { claudeAdapter } from '../../../providers/claude/index.js';
 import { codexAdapter } from '../../../providers/codex/index.js';
@@ -95,9 +95,11 @@ async function collectProviderList(context, dependencies) {
     for (const adapter of dependencies.getAdapters()) {
         const summary = createEmptySummary();
         const contentTypes = new Set();
+        const allMappings = [];
         for (const scope of scopes) {
             for (const mapping of dependencies.getSyncMappings(adapter, scope)) {
                 contentTypes.add(mapping.contentType);
+                allMappings.push(mapping);
             }
         }
         let detected = false;
@@ -114,7 +116,17 @@ async function collectProviderList(context, dependencies) {
                     continue;
                 }
                 summary.managed += 1;
-                const report = await dependencies.detectDrift(entry, scopeRoot.root);
+                const matchedMapping = allMappings.find((mapping) => {
+                    const normalizedEntry = normalizeToPosixPath(entry.providerPath);
+                    const normalizedDir = normalizeToPosixPath(mapping.providerDir);
+                    return (mapping.contentType === entry.contentType &&
+                        (normalizedEntry === normalizedDir ||
+                            normalizedEntry.startsWith(`${normalizedDir}/`)));
+                });
+                const copyTransform = matchedMapping?.transformCanonical
+                    ? { transformCanonical: matchedMapping.transformCanonical }
+                    : undefined;
+                const report = await dependencies.detectDrift(entry, scopeRoot.root, copyTransform);
                 if (report.state.status === 'in_sync') {
                     summary.inSync += 1;
                     continue;

package/dist/commands/providers/providers.types.d.ts

@@ -1,6 +1,6 @@
 import type { CommandContext, GlobalOptions } from '../../app/command-context.js';
 import type { SyncConfig } from '../../config/index.js';
-import type { DriftReport } from '../../drift/index.js';
+import type { CopyTransform, DriftReport } from '../../drift/index.js';
 import type { Manifest } from '../../manifest/index.js';
 import type { PathMapping, ProviderAdapter } from '../../providers/shared/index.js';
 import type { ConcreteScope, ContentType, Scope, SyncStrategy } from '../../shared/types.js';
@@ -24,7 +24,7 @@ export interface ProvidersListDependencies {
     getAdapters: () => ProviderAdapter[];
     getSyncMappings: (adapter: ProviderAdapter, scope: Scope) => PathMapping[];
     loadManifest: (manifestPath: string) => Promise<Manifest>;
-    detectDrift: (entry: Manifest['entries'][number], scopeRoot: string) => Promise<DriftReport>;
+    detectDrift: (entry: Manifest['entries'][number], scopeRoot: string, copyTransform?: CopyTransform) => Promise<DriftReport>;
 }
 export interface ProviderInspectMappingState {
     scope: ConcreteScope;
@@ -51,7 +51,7 @@ export interface ProvidersInspectDependencies {
     getAdapters: () => ProviderAdapter[];
     getSyncMappings: (adapter: ProviderAdapter, scope: Scope) => PathMapping[];
     loadManifest: (manifestPath: string) => Promise<Manifest>;
-    detectDrift: (entry: Manifest['entries'][number], scopeRoot: string) => Promise<DriftReport>;
+    detectDrift: (entry: Manifest['entries'][number], scopeRoot: string, copyTransform?: CopyTransform) => Promise<DriftReport>;
 }
 export interface ProvidersSetDependencies {
     buildCommandContext: (options: GlobalOptions) => CommandContext;

package/dist/commands/providers/providers.types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"providers.types.d.ts","sourceRoot":"","sources":["../../../src/commands/providers/providers.types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAC1E,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAChD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,KAAK,EAAE,WAAW,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACtE,OAAO,KAAK,EACV,aAAa,EACb,WAAW,EACX,KAAK,EACL,YAAY,EACb,MAAM,eAAe,CAAC;AAEvB,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,OAAO,CAAC;IAClB,eAAe,EAAE,YAAY,CAAC;IAC9B,YAAY,EAAE,WAAW,EAAE,CAAC;IAC5B,OAAO,EAAE,mBAAmB,CAAC;CAC9B;AAED,MAAM,WAAW,yBAAyB;IACxC,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,gBAAgB,EAAE,CAChB,KAAK,EAAE,aAAa,EACpB,OAAO,EAAE,cAAc,KACpB,OAAO,CAAC,MAAM,CAAC,CAAC;IACrB,WAAW,EAAE,MAAM,eAAe,EAAE,CAAC;IACrC,eAAe,EAAE,CAAC,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,KAAK,KAAK,WAAW,EAAE,CAAC;IAC3E,YAAY,EAAE,CAAC,YAAY,EAAE,MAAM,KAAK,OAAO,CAAC,QAAQ,CAAC,CAAC;IAC1D,WAAW,EAAE,CACX,KAAK,EAAE,QAAQ,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,EAClC,SAAS,EAAE,MAAM,KACd,OAAO,CAAC,WAAW,CAAC,CAAC;CAC3B;AAED,MAAM,WAAW,2BAA2B;IAC1C,KAAK,EAAE,aAAa,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,OAAO,CAAC;IAClB,eAAe,EAAE,YAAY,CAAC;IAC9B,eAAe,EAAE,WAAW,EAAE,CAAC;IAC/B,YAAY,EAAE,WAAW,EAAE,CAAC;IAC5B,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,QAAQ,EAAE,2BAA2B,EAAE,CAAC;CACzC;AAED,MAAM,WAAW,4BAA4B;IAC3C,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,gBAAgB,EAAE,CAChB,KAAK,EAAE,aAAa,EACpB,OAAO,EAAE,cAAc,KACpB,OAAO,CAAC,MAAM,CAAC,CAAC;IACrB,WAAW,EAAE,MAAM,eAAe,EAAE,CAAC;IACrC,eAAe,EAAE,CAAC,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,KAAK,KAAK,WAAW,EAAE,CAAC;IAC3E,YAAY,EAAE,CAAC,YAAY,EAAE,MAAM,KAAK,OAAO,CAAC,QAAQ,CAAC,CAAC;IAC1D,WAAW,EAAE,CACX,KAAK,EAAE,QAAQ,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,EAClC,SAAS,EAAE,MAAM,KACd,OAAO,CAAC,WAAW,CAAC,CAAC;CAC3B;AAED,MAAM,WAAW,wBAAwB;IACvC,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,gBAAgB,EAAE,CAChB,KAAK,EAAE,aAAa,EACpB,OAAO,EAAE,cAAc,KACpB,OAAO,CAAC,MAAM,CAAC,CAAC;IACrB,WAAW,EAAE,MAAM,eAAe,EAAE,CAAC;IACrC,cAAc,EAAE,CAAC,UAAU,EAAE,MAAM,KAAK,OAAO,CAAC,UAAU,CAAC,CAAC;IAC5D,cAAc,EAAE,CACd,UAAU,EAAE,MAAM,EAClB,MAAM,EAAE,UAAU,KACf,OAAO,CAAC,UAAU,CAAC,CAAC;CAC1B"}
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package/dist/commands/status/index.d.ts

@@ -1,7 +1,7 @@
 import { type CommandContext, type GlobalOptions } from '../../app/command-context.js';
 import { type CodexRoleStray } from '../shared/codex-strays.js';
 import { type MultiSelectChoice, type PromptContext } from '../shared/shared.prompts.js';
-import { type DriftReport } from '../../drift/index.js';
+import { type CopyTransform, type DriftReport } from '../../drift/index.js';
 import { type CanonicalEntry } from '../../engine/index.js';
 import type { Manifest } from '../../manifest/index.js';
 import { type CodexExtensionPlan } from '../../providers/codex/codec/sync-extension.js';
@@ -17,7 +17,7 @@ interface StatusDependencies {
     getAdapters: () => ProviderAdapter[];
     getActiveAdapters: (adapters: ProviderAdapter[], scopeRoot: string) => Promise<ProviderAdapter[]>;
     getSyncMappings: (adapter: ProviderAdapter, scope: Scope) => PathMapping[];
-    detectDrift: (entry: Manifest['entries'][number], scopeRoot: string) => Promise<DriftReport>;
+    detectDrift: (entry: Manifest['entries'][number], scopeRoot: string, copyTransform?: CopyTransform) => Promise<DriftReport>;
     detectStrays: (provider: string, providerDir: string, manifest: Manifest, canonicalEntries: CanonicalEntry[], mapping?: Pick<PathMapping, 'contentType' | 'providerExtension'>) => Promise<DriftReport[]>;
     detectCodexRoleStrays: (scopeRoot: string, canonicalEntries: CanonicalEntry[]) => Promise<CodexRoleStray[]>;
     computeCodexProjectExtensionPlan: (scopeRoot: string, canonicalEntries: CanonicalEntry[]) => Promise<CodexExtensionPlan>;

package/dist/commands/status/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/status/index.ts"],"names":[],"mappings":"AAEA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAK9B,OAAO,EACL,KAAK,cAAc,EAGpB,MAAM,+BAA+B,CAAC;AACvC,OAAO,EAEL,KAAK,iBAAiB,EACtB,KAAK,aAAa,EAEnB,MAAM,iCAAiC,CAAC;AAKzC,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,WAAW,EAGjB,MAAM,cAAc,CAAC;AACtB,OAAO,EAAE,KAAK,cAAc,EAAiB,MAAM,eAAe,CAAC;AAMnE,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAIhD,OAAO,EAEL,KAAK,kBAAkB,EAExB,MAAM,uCAAuC,CAAC;AAI/C,OAAO,EAGL,KAAK,WAAW,EAChB,KAAK,eAAe,EACrB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,KAAK,aAAa,EAGlB,KAAK,KAAK,EACX,MAAM,eAAe,CAAC;AAEvB,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAmBpC,UAAU,kBAAkB;IAC1B,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,gBAAgB,EAAE,CAChB,KAAK,EAAE,aAAa,EACpB,OAAO,EAAE,cAAc,KACpB,OAAO,CAAC,MAAM,CAAC,CAAC;IACrB,YAAY,EAAE,CAAC,YAAY,EAAE,MAAM,KAAK,OAAO,CAAC,QAAQ,CAAC,CAAC;IAC1D,YAAY,EAAE,CAAC,YAAY,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IAC1E,aAAa,EAAE,CACb,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,aAAa,KACjB,OAAO,CAAC,cAAc,EAAE,CAAC,CAAC;IAC/B,WAAW,EAAE,MAAM,eAAe,EAAE,CAAC;IACrC,iBAAiB,EAAE,CACjB,QAAQ,EAAE,eAAe,EAAE,EAC3B,SAAS,EAAE,MAAM,KACd,OAAO,CAAC,eAAe,EAAE,CAAC,CAAC;IAChC,eAAe,EAAE,CAAC,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,KAAK,KAAK,WAAW,EAAE,CAAC;IAC3E,WAAW,EAAE,CACX,KAAK,EAAE,QAAQ,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,EAClC,SAAS,EAAE,MAAM,EACjB,aAAa,CAAC,EAAE,aAAa,KAC1B,OAAO,CAAC,WAAW,CAAC,CAAC;IAC1B,YAAY,EAAE,CACZ,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,MAAM,EACnB,QAAQ,EAAE,QAAQ,EAClB,gBAAgB,EAAE,cAAc,EAAE,EAClC,OAAO,CAAC,EAAE,IAAI,CAAC,WAAW,EAAE,aAAa,GAAG,mBAAmB,CAAC,KAC7D,OAAO,CAAC,WAAW,EAAE,CAAC,CAAC;IAC5B,qBAAqB,EAAE,CACrB,SAAS,EAAE,MAAM,EACjB,gBAAgB,EAAE,cAAc,EAAE,KAC/B,OAAO,CAAC,cAAc,EAAE,CAAC,CAAC;IAC/B,gCAAgC,EAAE,CAChC,SAAS,EAAE,MAAM,EACjB,gBAAgB,EAAE,cAAc,EAAE,KAC/B,OAAO,CAAC,kBAAkB,CAAC,CAAC;IACjC,8BAA8B,EAAE,CAC9B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,kBAAkB,KACrB,OAAO,CAAC,OAAO,CAAC,CAAC;IACtB,mBAAmB,EAAE,CAAC,CAAC,SAAS,MAAM,EACpC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAC/B,GAAG,EAAE,aAAa,KACf,OAAO,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,CAAC;IACzB,aAAa,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,aAAa,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IACzE,UAAU,EAAE,CACV,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,QAAQ,EAClB,OAAO,CAAC,EAAE;QAAE,gBAAgB,CAAC,EAAE,OAAO,CAAA;KAAE,KACrC,OAAO,CAAC,QAAQ,CAAC,CAAC;IACvB,iBAAiB,EAAE,CAAC,OAAO,EAAE,WAAW,EAAE,KAAK,MAAM,CAAC;CACvD;AAED,UAAU,oBAAoB;IAC5B,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,WAAW,CAAC;IACpB,OAAO,EAAE,WAAW,CAAC;IACrB,QAAQ,CAAC,EAAE;QACT,IAAI,EAAE,YAAY,CAAC;QACnB,QAAQ,EAAE,MAAM,CAAC;QACjB,WAAW,CAAC,EAAE,MAAM,CAAC;KACtB,CAAC;CACH;AAieD,wBAAgB,mBAAmB,CACjC,SAAS,GAAE,OAAO,CAAC,kBAAkB,CAAM,GAC1C,OAAO,CAcT"}

package/dist/commands/status/index.js

@@ -4,7 +4,7 @@ import { adoptStrayToCanonical, isAdoptionConflictError, } from '../shared/adopt
 import { detectCodexRoleStrays, regenerateCodexAfterAdoption, } from '../shared/codex-strays.js';
 import { confirmAction, selectManyWithAbort, } from '../shared/shared.prompts.js';
 import { readGlobalOptions, resolveConcreteScopes, } from '../shared/shared.utils.js';
-import { detectDrift, detectStrays } from '../../drift/index.js';
+import { detectDrift, detectStrays, } from '../../drift/index.js';
 import { scanCanonical } from '../../engine/index.js';
 import { normalizeToPosixPath, resolveProjectRoot, resolveScopeRoot, } from '../../fs/paths.js';
 import { loadManifest, saveManifest } from '../../manifest/manager.js';
@@ -132,10 +132,15 @@ async function collectScopeReports(scope, context, dependencies) {
             if (!contentTypeAllowed(entry.contentType, scope)) {
                 continue;
             }
-            if (!mappings.some((mapping) => entryInsideMapping(entry.providerPath, mapping.providerDir))) {
+            const matchedMapping = mappings.find((mapping) => mapping.contentType === entry.contentType &&
+                entryInsideMapping(entry.providerPath, mapping.providerDir));
+            if (!matchedMapping) {
                 continue;
             }
-            reports.push(await dependencies.detectDrift(entry, scopeRoot));
+            const copyTransform = matchedMapping.transformCanonical
+                ? { transformCanonical: matchedMapping.transformCanonical }
+                : undefined;
+            reports.push(await dependencies.detectDrift(entry, scopeRoot, copyTransform));
         }
         for (const mapping of mappings) {
             for (const canonicalEntry of canonicalEntries) {

package/dist/commands/tools/remove/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/remove/index.ts"],"names":[],"mappings":"AAQA,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAK1C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAEL,KAAK,uBAAuB,EAE7B,MAAM,gBAAgB,CAAC;AA2CxB,wBAAgB,wBAAwB,CACtC,YAAY,GAAE,uBAA6C,EAC3D,gBAAgB,GAAE,oBAA8C,GAC/D,OAAO,CAsET"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/remove/index.ts"],"names":[],"mappings":"AAQA,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAM1C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAEL,KAAK,uBAAuB,EAE7B,MAAM,gBAAgB,CAAC;AA2CxB,wBAAgB,wBAAwB,CACtC,YAAY,GAAE,uBAA6C,EAC3D,gBAAgB,GAAE,oBAA8C,GAC/D,OAAO,CAwGT"}

package/dist/commands/tools/remove/index.js

@@ -4,6 +4,7 @@ import { buildCommandContext } from '../../../app/command-context.js';
 import { readGlobalOptions, resolveConcreteScopes, } from '../../shared/shared.utils.js';
 import { autoSync, } from '../../tools/shared/auto-sync.js';
 import { scanTools } from '../../tools/shared/scan-tools.js';
+import { readOatConfig, writeOatConfig } from '../../../config/oat-config.js';
 import { resolveAssetsRoot } from '../../../fs/assets.js';
 import { resolveProjectRoot, resolveScopeRoot } from '../../../fs/paths.js';
 import { Command } from 'commander';
@@ -65,6 +66,30 @@ export function createToolsRemoveCommand(dependencies = defaultDependencies, syn
         const scopes = resolveConcreteScopes(context.scope);
         const dryRun = opts.dryRun ?? false;
         const result = await removeTools(target, scopes, context.cwd, context.home, dryRun, dependencies);
+        if (!dryRun && result.removed.length > 0) {
+            const assetsRoot = await dependencies.resolveAssetsRoot();
+            const repoRoot = await resolveProjectRoot(context.cwd);
+            const config = await readOatConfig(repoRoot);
+            const installedPacks = new Set();
+            const configScopes = resolveConcreteScopes('all');
+            for (const scope of configScopes) {
+                const scopeRoot = await dependencies.resolveScopeRoot(scope, context.cwd, context.home);
+                const tools = await dependencies.scanTools({
+                    scope,
+                    scopeRoot,
+                    assetsRoot,
+                });
+                for (const tool of tools) {
+                    if (tool.pack !== 'custom') {
+                        installedPacks.add(tool.pack);
+                    }
+                }
+            }
+            await writeOatConfig(repoRoot, {
+                ...config,
+                tools: Object.fromEntries(VALID_PACKS.map((pack) => [pack, installedPacks.has(pack)])),
+            });
+        }
         if (result.notInstalled.length > 0) {
             if (context.json) {
                 logger.json({ target: describeTarget(target), dryRun, result });

package/dist/commands/tools/update/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/update/index.ts"],"names":[],"mappings":"AAYA,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAE1C,OAAO,KAAK,EAAY,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AAGvE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EACL,KAAK,YAAY,EACjB,KAAK,YAAY,EACjB,KAAK,uBAAuB,EAE7B,MAAM,gBAAgB,CAAC;AAuCxB,wBAAgB,wBAAwB,CACtC,YAAY,GAAE,uBAA6C,EAC3D,gBAAgB,GAAE,oBAA8C,GAC/D,OAAO,CAmGT;AAED,wBAAgB,qBAAqB,CACnC,MAAM,EAAE,YAAY,EACpB,MAAM,EAAE,YAAY,GACnB,OAAO,CAOT;AAED,wBAAgB,wBAAwB,CACtC,IAAI,EAAE,QAAQ,EACd,MAAM,EAAE,OAAO,GACd,MAAM,CAMR"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/update/index.ts"],"names":[],"mappings":"AAYA,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAE1C,OAAO,KAAK,EAAY,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AAIvE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EACL,KAAK,YAAY,EACjB,KAAK,YAAY,EACjB,KAAK,uBAAuB,EAE7B,MAAM,gBAAgB,CAAC;AAuCxB,wBAAgB,wBAAwB,CACtC,YAAY,GAAE,uBAA6C,EAC3D,gBAAgB,GAAE,oBAA8C,GAC/D,OAAO,CAsIT;AAED,wBAAgB,qBAAqB,CACnC,MAAM,EAAE,YAAY,EACpB,MAAM,EAAE,YAAY,GACnB,OAAO,CAOT;AAED,wBAAgB,wBAAwB,CACtC,IAAI,EAAE,QAAQ,EACd,MAAM,EAAE,OAAO,GACd,MAAM,CAMR"}

package/dist/commands/tools/update/index.js

@@ -5,6 +5,7 @@ import { copyDirWithStatus, copyFileWithStatus, } from '../../init/tools/shared/
 import { readGlobalOptions, resolveConcreteScopes, } from '../../shared/shared.utils.js';
 import { autoSync, } from '../../tools/shared/auto-sync.js';
 import { scanTools } from '../../tools/shared/scan-tools.js';
+import { readOatConfig, writeOatConfig } from '../../../config/oat-config.js';
 import { resolveAssetsRoot } from '../../../fs/assets.js';
 import { resolveProjectRoot, resolveScopeRoot } from '../../../fs/paths.js';
 import { Command } from 'commander';
@@ -62,15 +63,40 @@ export function createToolsUpdateCommand(dependencies = defaultDependencies, syn
         const scopes = resolveConcreteScopes(context.scope);
         const dryRun = opts.dryRun ?? false;
         const result = await updateTools(target, scopes, context.cwd, context.home, dryRun, dependencies);
+        const assetsRoot = dryRun ? null : await dependencies.resolveAssetsRoot();
         // Refresh ~/.oat/docs/ when the core pack is explicitly updated or
         // reconciled through --all (D3 requirement).
-        if (shouldRefreshCoreDocs(target, result) && !dryRun) {
-            const assetsRoot = await dependencies.resolveAssetsRoot();
+        if (shouldRefreshCoreDocs(target, result) && assetsRoot) {
             const userRoot = await dependencies.resolveScopeRoot('user', context.cwd, context.home);
             const docsSource = join(assetsRoot, 'docs');
             const docsDestination = join(userRoot, '.oat', 'docs');
             await dependencies.copyDirWithStatus(docsSource, docsDestination, true);
         }
+        if (assetsRoot && (target.kind === 'all' || target.kind === 'pack')) {
+            const repoRoot = await resolveProjectRoot(context.cwd);
+            const config = await readOatConfig(repoRoot);
+            const installedPacks = new Set();
+            const configScopes = resolveConcreteScopes('all');
+            for (const scope of configScopes) {
+                const scopeRoot = await dependencies.resolveScopeRoot(scope, context.cwd, context.home);
+                const tools = await dependencies.scanTools({
+                    scope,
+                    scopeRoot,
+                    assetsRoot,
+                });
+                for (const tool of tools) {
+                    if (tool.pack !== 'custom') {
+                        installedPacks.add(tool.pack);
+                    }
+                }
+            }
+            // Preserve unrelated shared config keys while rebuilding tools state
+            // from the repo-wide installed-pack scan.
+            await writeOatConfig(repoRoot, {
+                ...config,
+                tools: Object.fromEntries(VALID_PACKS.map((pack) => [pack, installedPacks.has(pack)])),
+            });
+        }
         if (result.notInstalled.length > 0) {
             if (context.json) {
                 logger.json({ target: describeTarget(target), dryRun, result });

package/dist/config/oat-config.d.ts

@@ -13,6 +13,7 @@ export interface OatArchiveConfig {
     s3SyncOnComplete?: boolean;
     summaryExportPath?: string;
 }
+export type OatToolsConfig = Partial<Record<'core' | 'ideas' | 'docs' | 'workflows' | 'utility' | 'project-management' | 'research', boolean>>;
 export interface OatConfig {
     version: number;
     worktrees?: {
@@ -23,6 +24,7 @@ export interface OatConfig {
     };
     git?: OatGitConfig;
     archive?: OatArchiveConfig;
+    tools?: OatToolsConfig;
     documentation?: OatDocumentationConfig;
     localPaths?: string[];
     autoReviewAtCheckpoints?: boolean;

package/dist/config/oat-config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"oat-config.d.ts","sourceRoot":"","sources":["../../src/config/oat-config.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,sBAAsB;IACrC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,2BAA2B,CAAC,EAAE,OAAO,CAAC;CACvC;AAED,MAAM,WAAW,YAAY;IAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB;AAED,MAAM,WAAW,gBAAgB;IAC/B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,iBAAiB,CAAC,EAAE,MAAM,CAAC;CAC5B;AAED,MAAM,MAAM,cAAc,GAAG,OAAO,CAClC,MAAM,CACF,MAAM,GACN,OAAO,GACP,MAAM,GACN,WAAW,GACX,SAAS,GACT,oBAAoB,GACpB,UAAU,EACZ,OAAO,CACR,CACF,CAAC;AAEF,MAAM,WAAW,SAAS;IACxB,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IAC7B,QAAQ,CAAC,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IAC5B,GAAG,CAAC,EAAE,YAAY,CAAC;IACnB,OAAO,CAAC,EAAE,gBAAgB,CAAC;IAC3B,KAAK,CAAC,EAAE,cAAc,CAAC;IACvB,aAAa,CAAC,EAAE,sBAAsB,CAAC;IACvC,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;IACtB,uBAAuB,CAAC,EAAE,OAAO,CAAC;CACnC;AAED,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC9B,iBAAiB,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAClC,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B;AAED,MAAM,WAAW,UAAU;IACzB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B;AAED,MAAM,WAAW,uBAAuB;IACtC,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,MAAM,EAAE,QAAQ,GAAG,SAAS,GAAG,OAAO,CAAC;CACxC;AA+OD,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,SAAS,GAAG,MAAM,EAAE,CAE7D;AAED,wBAAsB,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,SAAS,CAAC,CAaxE;AAED,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,cAAc,CAAC,CAazB;AAED,wBAAsB,cAAc,CAClC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,SAAS,GAChB,OAAO,CAAC,IAAI,CAAC,CAIf;AAED,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,cAAc,GACrB,OAAO,CAAC,IAAI,CAAC,CAIf;AAED,wBAAsB,oBAAoB,CACxC,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,uBAAuB,CAAC,CAkBlC;AAED,wBAAsB,gBAAgB,CACpC,QAAQ,EAAE,MAAM,EAChB,mBAAmB,EAAE,MAAM,GAC1B,OAAO,CAAC,IAAI,CAAC,CAaf;AAED,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE;IAAE,UAAU,CAAC,EAAE,MAAM,CAAA;CAAE,GAChC,OAAO,CAAC,IAAI,CAAC,CAYf;AAsBD,wBAAsB,cAAc,CAClC,aAAa,EAAE,MAAM,GACpB,OAAO,CAAC,UAAU,CAAC,CAarB;AAED,wBAAsB,eAAe,CACnC,aAAa,EAAE,MAAM,EACrB,MAAM,EAAE,UAAU,GACjB,OAAO,CAAC,IAAI,CAAC,CAIf;AAED,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,MAAM,EAChB,aAAa,EAAE,MAAM,GACpB,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAQxB;AAED,wBAAsB,aAAa,CACjC,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,IAAI,CAAC,CAMf;AAED,wBAAsB,eAAe,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAMrE;AAED,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CA6B5D"}

package/dist/config/oat-config.js

@@ -93,6 +93,26 @@ function normalizeOatConfig(parsed) {
             next.archive = archive;
         }
     }
+    if (isRecord(parsed.tools)) {
+        const validPacks = [
+            'core',
+            'ideas',
+            'docs',
+            'workflows',
+            'utility',
+            'project-management',
+            'research',
+        ];
+        const tools = {};
+        for (const pack of validPacks) {
+            if (typeof parsed.tools[pack] === 'boolean') {
+                tools[pack] = parsed.tools[pack];
+            }
+        }
+        if (Object.keys(tools).length > 0) {
+            next.tools = tools;
+        }
+    }
     if (isRecord(parsed.documentation)) {
         const doc = {};
         if (typeof parsed.documentation.root === 'string' &&

package/dist/drift/detector.d.ts

@@ -1,4 +1,7 @@
 import type { ManifestEntry } from '../manifest/manifest.types.js';
 import type { DriftReport } from './drift.types.js';
-export declare function detectDrift(entry: ManifestEntry, scopeRoot: string): Promise<DriftReport>;
+export interface CopyTransform {
+    transformCanonical: (content: string, canonicalPath: string) => string;
+}
+export declare function detectDrift(entry: ManifestEntry, scopeRoot: string, copyTransform?: CopyTransform): Promise<DriftReport>;
 //# sourceMappingURL=detector.d.ts.map

package/dist/drift/detector.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"detector.d.ts","sourceRoot":"","sources":["../../src/drift/detector.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,0BAA0B,CAAC;AAE9D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAcjD,wBAAsB,WAAW,CAC/B,KAAK,EAAE,aAAa,EACpB,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC,WAAW,CAAC,CAmEtB"}
+{"version":3,"file":"detector.d.ts","sourceRoot":"","sources":["../../src/drift/detector.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,0BAA0B,CAAC;AAE9D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,WAAW,aAAa;IAC5B,kBAAkB,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,KAAK,MAAM,CAAC;CACxE;AAcD,wBAAsB,WAAW,CAC/B,KAAK,EAAE,aAAa,EACpB,SAAS,EAAE,MAAM,EACjB,aAAa,CAAC,EAAE,aAAa,GAC5B,OAAO,CAAC,WAAW,CAAC,CAkFtB"}

package/dist/drift/detector.js

@@ -1,6 +1,6 @@
-import { lstat, readlink, stat } from 'node:fs/promises';
+import { lstat, readFile, readlink, stat } from 'node:fs/promises';
 import { dirname, resolve } from 'node:path';
-import { computeContentHash } from '../manifest/hash.js';
+import { computeContentHash, computeStringHash } from '../manifest/hash.js';
 function createReport(entry, state) {
     return {
         canonical: entry.canonicalPath,
@@ -9,7 +9,7 @@ function createReport(entry, state) {
         state,
     };
 }
-export async function detectDrift(entry, scopeRoot) {
+export async function detectDrift(entry, scopeRoot, copyTransform) {
     const providerPath = resolve(scopeRoot, entry.providerPath);
     const canonicalPath = resolve(scopeRoot, entry.canonicalPath);
     // Missing check must run first, before strategy-specific branches.
@@ -62,6 +62,17 @@ export async function detectDrift(entry, scopeRoot) {
     if (entry.contentHash === currentHash) {
         return createReport(entry, { status: 'in_sync' });
     }
+    // When the manifest hash is stale (e.g. frontmatter-only edits to the
+    // canonical source that don't change the rendered output), re-derive the
+    // expected provider content from the current canonical + transform and
+    // compare that instead.
+    if (copyTransform && entry.isFile) {
+        const canonicalContent = await readFile(canonicalPath, 'utf8');
+        const rendered = copyTransform.transformCanonical(canonicalContent, entry.canonicalPath);
+        if (computeStringHash(rendered) === currentHash) {
+            return createReport(entry, { status: 'in_sync' });
+        }
+    }
     return createReport(entry, {
         status: 'drifted',
         reason: 'modified',

package/dist/drift/index.d.ts

@@ -1,4 +1,5 @@
 export { detectDrift } from './detector.js';
+export type { CopyTransform } from './detector.js';
 export type { DriftReport, DriftState } from './drift.types.js';
 export { detectStrays } from './strays.js';
 //# sourceMappingURL=index.d.ts.map

package/dist/drift/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/drift/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AACzC,YAAY,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAC7D,OAAO,EAAE,YAAY,EAAE,MAAM,UAAU,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/drift/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AACzC,YAAY,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAChD,YAAY,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAC7D,OAAO,EAAE,YAAY,EAAE,MAAM,UAAU,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@open-agent-toolkit/cli",
-  "version": "0.0.18",
+  "version": "0.0.20",
   "private": false,
   "description": "Open Agent Toolkit CLI",
   "homepage": "https://github.com/voxmedia/open-agent-toolkit/tree/main/packages/cli",