@open-agent-toolkit/cli 0.2.45 → 0.2.46

package/assets/bundle-metadata.json

@@ -1,4 +1,4 @@
 {
   "schemaVersion": 1,
-  "oatVersion": "0.2.45"
+  "oatVersion": "0.2.46"
 }

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

@@ -140,6 +140,12 @@ Two independent facts describe a pack:
   release manifest declares for that pack and scope, its presence, and its
   version or content digest.
 
+Versioned skills and agents must match on both version metadata and canonical
+content. A same-version content change is therefore reported as outdated rather
+than current. Content comparison ignores the executable-bit normalization OAT
+intentionally applies while materializing managed scripts, but still detects
+file content, entry-type, and symlink-target changes.
+
 Commands report both. `oat tools list` and `oat tools info` show placement,
 intent source, and completeness. `oat status` and `oat doctor` report drift
 between intent and inventory with a scoped recovery command.
@@ -182,11 +188,12 @@ without qualification. Install the pack at **project scope** when you need its
 agents; `oat tools update` cannot repair this, because it is a scope limitation
 rather than drift.
 
-Repository templates under `.oat/templates/` are **owner overrides**. Once a
-project-scope template exists, OAT will not rewrite it: the managed default now
-lives at user scope and in the bundle. Delete the repository copy to resume
-managed-default behavior. `oat status` and `oat doctor` report retained
-overrides so the divergence is visible rather than silent.
+Repository templates under `.oat/templates/` are **owner-owned seeds**. OAT
+compares a source-backed seed with its bundled default: a byte-equivalent copy
+is reported as current, while an edited copy is retained and reported as a
+`retained-override`. OAT will not rewrite the retained copy. Delete a repository
+template only when you intentionally want the bundled default seeded again;
+never delete edited mutable seed content merely to clear the diagnostic.
 
 ### Evolving pack membership
 
@@ -454,8 +461,15 @@ Key behavior:
 - Every pack's fresh-install default is user scope (`defaultScope` in the release manifest); existing installs keep their current placement on re-install, so a re-install never moves a pack between scopes or creates a second copy at the other one. This applies to the per-pack subcommands too: a bare `oat tools install docs` in a repository where `docs` is already at project scope stays at project scope, and only an explicit `--scope` overrides that
 - Removing a pack from a scope happens only when you explicitly choose a narrower end-state in the interactive flow (e.g. a pack at `both` set to `project` only). All staged removals are shown in a single change summary and applied only after one batch confirmation — declining makes no changes
 - Non-interactive installs (including `--scope project`, `--scope user`, and the default pack set) are strictly additive and never remove a pack from a scope. Removal is interactive-only
-- Tracks installed vs bundled skill versions and reports outdated skills
+- Tracks installed versus bundled skill and agent versions and canonical
+  content, reporting same-version content drift as outdated while ignoring
+  expected executable-bit normalization
 - Writes pack intent into the config file for the scope you installed into: a project install sets `tools.<pack>: true` in `.oat/config.json`, and a user install sets it in `~/.oat/config.json`. A user-only install never writes repository config
+- When a project install discovers existing project-scoped packs whose intent
+  is missing, it writes those exact intents in canonical pack order. Human
+  output prints `Adopted project tool pack: <pack>` once per adopted pack;
+  JSON output adds `adoptedPacks` only when the list is non-empty. This is pack
+  intent reconciliation, not repository PJM adoption
 - A user-only install needs no Git repository and performs no repository writes
 - Refreshes the managed `OAT tools` section in the repository-root `AGENTS.md` **only for project-scope runs of the aggregate `oat tools install`**. The per-pack subcommands (`oat tools install workflows`, `oat tools install docs`, and the rest) never write `AGENTS.md`, at either scope
 - Repository `AGENTS.md` guidance for project management is owned by adoption, not by pack placement. Installing the `project-management` pack no longer upserts a managed `OAT project-management` section; `oat pjm init` writes that repository guidance when the repository actually adopts PJM
@@ -474,12 +488,17 @@ Key behavior:
 
 - Accepts a tool name, `--pack <pack>`, or `--all` (mutually exclusive)
 - With no target, exits without mutation and suggests the explicit bulk command `oat tools update --all`; invalid packs and conflicting targets keep their own targeted diagnostics
-- Compares installed versions against bundled versions and copies updated assets
+- Compares installed versions and canonical content against bundled assets and
+  copies updates; equal version metadata does not hide content drift
 - For `--pack <pack>` and `--all`, an already-installed pack is reconciled to the **current** release membership in the scopes where it is installed, adding newly bundled skills, agents, templates, and scripts
 - A pack whose managed assets are all missing but whose intent is still declared is repaired from intent rather than skipped
 - Managed template and script companions are refreshed at **user** scope. A project-scope repository template is an owner override and is left alone
 - Non-versioned assets are compared by content digest, so an identical refresh is a no-op instead of a rewrite
 - Update persists inferred legacy intent only after a successful explicit mutation, so a read never rewrites your config
+- A successful project-scope update reports the exact newly adopted legacy pack
+  intents in canonical order. Human output uses
+  `Adopted project tool pack: <pack>`; JSON output adds the optional
+  `adoptedPacks` array only when at least one intent was written
 - `--scope all` outside a Git repository completes the user-scope work instead of failing. Unlike `oat status` and `oat doctor`, update skips project scope silently and does not name it in the result; an explicitly requested `--scope project` outside a repository is still a hard failure
 - Dry-run mode with `--dry-run`; auto-sync after mutations by default
 - Use `--no-sync` to skip auto-sync
@@ -735,8 +754,9 @@ Removal and migration use the symmetric contract: the follow-up sync prunes exac
 User-scope tool packs and explicit PJM adoption changed several defaults and
 exit codes. Nothing here is data-destructive, and legacy config keeps working —
 `tools.<pack>: false` still parses, complete pre-adoption PJM scaffolds are
-grandfathered as `inferred-legacy`, and no CLI flag was removed or renamed. But
-several commands you already run behave differently.
+grandfathered as `inferred-legacy`, and existing installs remain additive. One
+inert per-pack install flag was removed, and several commands you already run
+behave differently.
 
 ### Install scope defaults flipped to user
 
@@ -781,6 +801,26 @@ is not installed. Test for a truthy value instead. Legacy `false` values that
 already exist in a config file are still read (see
 [Legacy `false` intent](#legacy-false-intent)) — they are just never written.
 
+Direct config writes now enforce the same true-or-absent contract.
+`oat config set tools.<pack> false` exits `1` without changing the config. To
+remove a project-scoped pack and clear its intent, run:
+
+```bash
+oat tools remove --pack <pack> --scope project
+```
+
+Existing legacy `false` values remain readable migration input.
+
+### Per-pack install `--force` was removed
+
+`oat tools install <pack> --force` is now rejected as an unknown option. The
+flag was inert in the unified additive lifecycle. To reconcile installed
+assets, use the scoped update command instead:
+
+```bash
+oat tools update --pack <pack> --scope <scope>
+```
+
 ### Per-pack install `--json` changed shape
 
 The per-pack subcommands (`oat tools install docs`, `oat tools install
@@ -803,6 +843,12 @@ above. The previous single-scope payload's `scope`, `targetRoot`, `assetsRoot`,
 keying on them reads `undefined` rather than failing. Read `scopes` for the
 scopes acted on, and `results[].request.scopeRoot` for the target root of each.
 
+When a project-scope aggregate install, direct pack install, or update adopts
+missing legacy pack intents, the same single payload also contains
+`"adoptedPacks": ["docs", "workflows"]`. The field is omitted when nothing was
+adopted, and entries follow the manifest's canonical pack order. Human output
+reports the same set as one `Adopted project tool pack: <pack>` line per pack.
+
 ### Other behavior changes worth knowing
 
 - `oat tools remove --pack <pack>` deletes every managed asset the release

package/assets/docs/reference/troubleshooting.md

@@ -77,8 +77,10 @@ Use [Instruction Sync](../provider-sync/instruction-sync.md) for the full strate
 
 - Run `oat init tools` to install/update bundled OAT tool packs.
 - In TTY mode, select which outdated skills to update when prompted.
-- In non-interactive mode, rerun the relevant pack subcommand with `--force` if you want to overwrite outdated installed skills.
-- For pack-level drift rather than a single skill, prefer the scoped command doctor prints: `oat tools update --pack <pack> --scope <scope>`.
+- In non-interactive mode, run the scoped command doctor prints:
+  `oat tools update --pack <pack> --scope <scope>`.
+- Per-pack install commands no longer accept the previously inert `--force`
+  option.
 
 ## `sync` reports an unsafe provider parent
 
@@ -147,18 +149,23 @@ Both commands report managed pack state with a scoped recovery command:
 
 - `partial` — some managed assets are missing, or intent is declared with none
   installed. Fix with `oat tools update --pack <pack> --scope <scope>`.
-- `stale` — installed assets are behind the bundled release. Same fix.
+- `stale` — installed assets are behind the bundled release, or a managed skill
+  or agent has the bundled version metadata but different canonical content.
+  Expected executable-bit normalization on managed scripts is ignored. Fix with
+  the same scoped update command.
 - `newer` — installed assets are ahead of the bundle. This is informational and
   usually means the CLI is older than the assets; update the CLI rather than
   downgrading the pack.
-- `retained-override` — an owner-owned seeded asset exists at the scope, so the
-  managed default is intentionally not applied there. This covers repository
-  templates under `.oat/templates/` **and** seeded content such as
-  `.oat/ideas/backlog.md` and `.oat/ideas/scratchpad.md`. Deleting the file is
-  the right move only for a **template** you want OAT to manage again; never
-  delete seeded content you have edited, because the next install or update
-  reseeds the bundled default in its place and your edits are gone. The finding
-  is informational and carries no recovery command for exactly that reason.
+- `retained-override` — a source-backed owner-owned seed differs from its
+  bundled default, so OAT retains the edited copy instead of overwriting it. A
+  bundle-equal seed is current and does not produce this finding. Retained
+  overrides cover repository templates under `.oat/templates/` **and** seeded
+  content such as `.oat/ideas/backlog.md` and `.oat/ideas/scratchpad.md`.
+  Deleting the file is the right move only for a **template** you intentionally
+  want OAT to seed from the bundle again; never delete seeded content you have
+  edited, because the next install or update reseeds the bundled default in its
+  place and your edits are gone. The finding is informational and carries no
+  recovery command for exactly that reason.
 - `user-agent-unmaterialized` — the pack installed canonical agents into
   `~/.agents/agents/`, but user scope materializes no provider view for them
   beyond the bundled managed role files. `oat tools update` cannot fix this.

package/assets/public-package-versions.json

@@ -1,6 +1,6 @@
 {
-  "cli": "0.2.45",
-  "docs-config": "0.2.45",
-  "docs-theme": "0.2.45",
-  "docs-transforms": "0.2.45"
+  "cli": "0.2.46",
+  "docs-config": "0.2.46",
+  "docs-theme": "0.2.46",
+  "docs-transforms": "0.2.46"
 }

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

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

@@ -1701,8 +1701,11 @@ async function setConfigValue(repoRoot, userConfigDir, key, rawValue, surface, d
     }
     if (key.startsWith('tools.')) {
         const packName = key.slice('tools.'.length);
+        if (rawValue.trim().toLowerCase() !== 'true') {
+            throw new Error(`Pack intent '${key}' can only be declared with true. To remove the pack and clear its intent, run: oat tools remove --pack ${packName} --scope project`);
+        }
         const tools = { ...config.tools };
-        tools[packName] = rawValue.trim().toLowerCase() === 'true';
+        tools[packName] = true;
         await dependencies.writeOatConfig(repoRoot, {
             ...config,
             tools,

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

@@ -60,6 +60,7 @@ export interface InitToolsDependencies {
 interface InitToolsRunMetadata {
     affectedScopes: ConcreteScope[];
     appliedScopes: ConcreteScope[];
+    adoptedPacks: ToolPack[];
 }
 interface PackScopeChange {
     pack: ToolPack;

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

@@ -1 +1 @@
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package/dist/commands/init/tools/index.js

@@ -411,15 +411,19 @@ function buildPackEndStateChoices(pack, currentLocation, defaultEndState) {
     const rest = annotated.filter((choice) => choice.value !== defaultEndState);
     return defaultChoice ? [defaultChoice, ...rest] : annotated;
 }
-function reportSuccess(context, packs, syncScopes) {
+function reportSuccess(context, packs, syncScopes, adoptedPacks) {
     if (context.json) {
         context.logger.json({
             status: 'ok',
             installedPacks: packs,
             syncScopes,
+            ...(adoptedPacks.length > 0 ? { adoptedPacks } : {}),
         });
         return;
     }
+    for (const pack of adoptedPacks) {
+        context.logger.info(`Adopted project tool pack: ${pack}`);
+    }
     context.logger.info(`Installed tool packs: ${packs.map(({ pack, scope }) => `${pack} (${formatInstalledLocation(scope)})`).join(', ')}`);
     syncScopes.forEach((scope, index) => {
         context.logger.info(`${index === 0 ? 'Run' : 'Also run'}: oat sync --scope ${scope}`);
@@ -515,7 +519,11 @@ export async function runInitTools(context, dependencies) {
             selectedPacks.push('project-management');
         }
         if (selectedPacks.length === 0) {
-            lastRunInitToolsMetadata = { affectedScopes: [], appliedScopes: [] };
+            lastRunInitToolsMetadata = {
+                affectedScopes: [],
+                appliedScopes: [],
+                adoptedPacks: [],
+            };
             if (!context.json) {
                 context.logger.info('No tool packs selected.');
             }
@@ -838,11 +846,19 @@ export async function runInitTools(context, dependencies) {
         const appliedScopes = [
             ...new Set(packScopeInfo.flatMap(({ scope }) => scopesForEndState(scope))),
         ];
+        const adoptedPacks = projectRoot && appliedScopes.includes('project')
+            ? (await reconcileProjectToolsConfig({
+                repoRoot: projectRoot,
+                cwd: context.cwd,
+                home: context.home,
+            }, dependencies)).adoptedPacks
+            : [];
         lastRunInitToolsMetadata = {
             affectedScopes: affectedScopesList,
             appliedScopes,
+            adoptedPacks,
         };
-        reportSuccess(context, packScopeInfo, affectedScopesList);
+        reportSuccess(context, packScopeInfo, affectedScopesList, adoptedPacks);
         process.exitCode = 0;
         return selectedPacks;
     }
@@ -912,7 +928,7 @@ function createReconciledPackCommand(pack, dependencies) {
     const base = new Command(pack).description(descriptions[pack]);
     const packCommand = pack === 'core' ? base : withScopeOption(base);
     return packCommand
-        .option('--force', 'Reconcile managed assets to bundled content')
+        .allowUnknownOption(false)
         .action(async (_options, command) => {
         const context = dependencies.buildCommandContext(readGlobalOptions(command));
         try {
@@ -946,15 +962,26 @@ function createReconciledPackCommand(pack, dependencies) {
             // Project-scope placement installs capability only. The
             // project-management and decisions AGENTS sections are written by the
             // explicit adoption action (`oat pjm init`), never by pack placement.
+            const adoptedPacks = scopes.includes('project')
+                ? (await reconcileProjectToolsConfig({
+                    repoRoot: await dependencies.resolveProjectRoot(context.cwd),
+                    cwd: context.cwd,
+                    home: context.home,
+                }, dependencies)).adoptedPacks
+                : [];
             if (context.json) {
                 context.logger.json({
                     status: 'ok',
                     pack,
                     scopes,
                     results,
+                    ...(adoptedPacks.length > 0 ? { adoptedPacks } : {}),
                 });
             }
             else {
+                for (const adoptedPack of adoptedPacks) {
+                    context.logger.info(`Adopted project tool pack: ${adoptedPack}`);
+                }
                 context.logger.info(`Installed ${pack} tool pack.`);
                 for (const result of results) {
                     context.logger.info(`Scope: ${result.request.scope}`);
@@ -1045,10 +1072,12 @@ export function createInitToolsCommand(overrides = {}) {
                 scanTools: dependencies.scanTools,
             }),
         ];
-    for (const packCommand of packCommands) {
-        packCommand.hook('postAction', async (_thisCommand, actionCommand) => {
-            await reconcileAfterInstall(actionCommand);
-        });
+    if (!dependencies.reconcilePacks) {
+        for (const packCommand of packCommands) {
+            packCommand.hook('postAction', async (_thisCommand, actionCommand) => {
+                await reconcileAfterInstall(actionCommand);
+            });
+        }
     }
     const command = new Command('tools').description('Install OAT tool packs (core, ideas, docs, workflows, utility, project-management, research, brainstorm)');
     for (const packCommand of packCommands) {
@@ -1059,7 +1088,6 @@ export function createInitToolsCommand(overrides = {}) {
         const selectedPacks = await runInitTools(context, dependencies);
         appliedScopesByCommand.set(actionCommand, lastRunInitToolsMetadata?.appliedScopes ?? []);
         setInstalledCanonicalPaths(actionCommand, canonicalPathsForPacks(selectedPacks));
-        await reconcileAfterInstall(actionCommand);
     });
     return command;
 }

package/dist/commands/tools/shared/pack-inventory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pack-inventory.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/shared/pack-inventory.ts"],"names":[],"mappings":"AAYA,OAAO,EACL,KAAK,aAAa,EAEnB,MAAM,eAAe,CAAC;AAIvB,OAAO,EAEL,KAAK,gBAAgB,EAEtB,MAAM,sBAAsB,CAAC;AAC9B,OAAO,KAAK,EACV,mBAAmB,EACnB,eAAe,EACf,gBAAgB,EAChB,QAAQ,EACT,MAAM,SAAS,CAAC;AAEjB,MAAM,WAAW,kBAAkB;IACjC,UAAU,EAAE,mBAAmB,CAAC;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,eAAe,CAAC;IACxB,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,EACA,uBAAuB,GACvB,iBAAiB,GACjB,0BAA0B,GAC1B,2BAA2B,CAAC;IAChC,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,QAAQ,CAAC,EAAE,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC;CACjC;AAED,MAAM,WAAW,mBAAmB;IAClC,IAAI,EAAE,QAAQ,CAAC;IACf,KAAK,EAAE,aAAa,CAAC;IACrB,MAAM,EAAE,gBAAgB,CAAC;IACzB,YAAY,EAAE,gBAAgB,CAAC;IAC/B,MAAM,EAAE,kBAAkB,EAAE,CAAC;IAC7B,WAAW,EAAE,cAAc,EAAE,CAAC;CAC/B;AAED,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,QAAQ,CAAC;IACf,SAAS,EAAE,SAAS,GAAG,MAAM,GAAG,MAAM,GAAG,aAAa,CAAC;IACvD,MAAM,EAAE,mBAAmB,EAAE,CAAC;IAC9B,WAAW,EAAE,cAAc,EAAE,CAAC;CAC/B;AAED,MAAM,WAAW,wBAAwB;IACvC,IAAI,EAAE,QAAQ,CAAC;IACf,KAAK,EAAE,aAAa,CAAC;IACrB,SAAS,EAAE,MAAM,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,kBAAkB;IACjC,IAAI,EAAE,QAAQ,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAoLD,wBAAsB,mBAAmB,CACvC,KAAK,EAAE,wBAAwB,GAC9B,OAAO,CAAC,mBAAmB,CAAC,CAmC9B;AAED,wBAAgB,8BAA8B,CAC5C,SAAS,EAAE,mBAAmB,GAC7B,OAAO,CAUT;AAED,wBAAsB,aAAa,CACjC,KAAK,EAAE,kBAAkB,GACxB,OAAO,CAAC,aAAa,CAAC,CA0DxB"}
+{"version":3,"file":"pack-inventory.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/shared/pack-inventory.ts"],"names":[],"mappings":"AAaA,OAAO,EACL,KAAK,aAAa,EAEnB,MAAM,eAAe,CAAC;AAIvB,OAAO,EAEL,KAAK,gBAAgB,EAEtB,MAAM,sBAAsB,CAAC;AAC9B,OAAO,KAAK,EACV,mBAAmB,EACnB,eAAe,EACf,gBAAgB,EAChB,QAAQ,EACT,MAAM,SAAS,CAAC;AAEjB,MAAM,WAAW,kBAAkB;IACjC,UAAU,EAAE,mBAAmB,CAAC;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,eAAe,CAAC;IACxB,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,EACA,uBAAuB,GACvB,iBAAiB,GACjB,0BAA0B,GAC1B,2BAA2B,CAAC;IAChC,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,QAAQ,CAAC,EAAE,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC;CACjC;AAED,MAAM,WAAW,mBAAmB;IAClC,IAAI,EAAE,QAAQ,CAAC;IACf,KAAK,EAAE,aAAa,CAAC;IACrB,MAAM,EAAE,gBAAgB,CAAC;IACzB,YAAY,EAAE,gBAAgB,CAAC;IAC/B,MAAM,EAAE,kBAAkB,EAAE,CAAC;IAC7B,WAAW,EAAE,cAAc,EAAE,CAAC;CAC/B;AAED,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,QAAQ,CAAC;IACf,SAAS,EAAE,SAAS,GAAG,MAAM,GAAG,MAAM,GAAG,aAAa,CAAC;IACvD,MAAM,EAAE,mBAAmB,EAAE,CAAC;IAC9B,WAAW,EAAE,cAAc,EAAE,CAAC;CAC/B;AAED,MAAM,WAAW,wBAAwB;IACvC,IAAI,EAAE,QAAQ,CAAC;IACf,KAAK,EAAE,aAAa,CAAC;IACrB,SAAS,EAAE,MAAM,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,kBAAkB;IACjC,IAAI,EAAE,QAAQ,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AA8QD,wBAAsB,mBAAmB,CACvC,KAAK,EAAE,wBAAwB,GAC9B,OAAO,CAAC,mBAAmB,CAAC,CAmC9B;AAED,wBAAgB,8BAA8B,CAC5C,SAAS,EAAE,mBAAmB,GAC7B,OAAO,CAUT;AAED,wBAAsB,aAAa,CACjC,KAAK,EAAE,kBAAkB,GACxB,OAAO,CAAC,aAAa,CAAC,CA0DxB"}

package/dist/commands/tools/shared/pack-inventory.js

@@ -1,9 +1,9 @@
-import { lstat } from 'node:fs/promises';
+import { lstat, readdir, readlink } from 'node:fs/promises';
 import { join } from 'node:path';
 import { compareVersions } from '../../init/tools/shared/version.js';
 import { getAgentVersion, getSkillVersion } from '../../shared/frontmatter.js';
 import { readOatConfig } from '../../../config/oat-config.js';
-import { resolveManagedScopeRoots, validateManagedPath, } from '../../../fs/paths.js';
+import { resolveManagedScopeRoots, validateManagedPath, validateRealPathWithinScope, } from '../../../fs/paths.js';
 import { USER_SCOPE_MANAGED_AGENT_FILES, } from '../../../shared/types.js';
 import { digestDirectory, digestFile } from './content-digest.js';
 import { getPackDefinition } from './pack-manifest.js';
@@ -29,14 +29,62 @@ async function inventoryVersionedAsset(definition, installedPath, bundledPath) {
         readVersion(installedPath),
         readVersion(bundledPath),
     ]);
+    const versionStatus = compareVersions(installedVersion, bundledVersion);
+    const contentMatches = versionStatus !== 'current'
+        ? null
+        : definition.kind === 'skill'
+            ? await canonicalDirectoryMatches(installedPath, bundledPath)
+            : await canonicalFileMatches(installedPath, bundledPath);
     return {
         definition,
         path: installedPath,
-        status: compareVersions(installedVersion, bundledVersion),
+        status: versionStatus === 'current' && !contentMatches
+            ? 'outdated'
+            : versionStatus,
         installedVersion,
         bundledVersion,
     };
 }
+async function canonicalFileMatches(installedPath, bundledPath) {
+    const [installedDigest, bundledDigest] = await Promise.all([
+        digestFile(installedPath, 0o644),
+        digestFile(bundledPath, 0o644),
+    ]);
+    return installedDigest === bundledDigest;
+}
+async function canonicalDirectoryMatches(installedRoot, bundledRoot) {
+    const entries = await readdir(bundledRoot, { withFileTypes: true });
+    for (const entry of entries) {
+        const installedPath = join(installedRoot, entry.name);
+        const bundledPath = join(bundledRoot, entry.name);
+        if (!(await pathExists(installedPath)))
+            return false;
+        const installedMetadata = await lstat(installedPath);
+        if (entry.isDirectory()) {
+            if (!installedMetadata.isDirectory() ||
+                !(await canonicalDirectoryMatches(installedPath, bundledPath))) {
+                return false;
+            }
+            continue;
+        }
+        if (entry.isFile()) {
+            if (!installedMetadata.isFile() ||
+                !(await canonicalFileMatches(installedPath, bundledPath))) {
+                return false;
+            }
+            continue;
+        }
+        if (entry.isSymbolicLink()) {
+            if (!installedMetadata.isSymbolicLink() ||
+                (await readlink(installedPath)) !== (await readlink(bundledPath))) {
+                return false;
+            }
+            continue;
+        }
+        throw new Error(`Unsupported filesystem entry in pack asset: ${bundledPath}`);
+    }
+    return true;
+}
 async function inventoryStaticAsset(definition, installedPath, bundledPath) {
     const [installedDigest, bundledDigest] = definition.kind === 'directory'
         ? await Promise.all([
@@ -72,28 +120,40 @@ async function inventoryAsset(definition, scope, scopeRoot, assetsRoot, managedR
         };
     }
     if (definition.ownership[scope] === 'seed-if-missing') {
-        if (definition.generation === 'projects-config-default') {
-            const config = await readOatConfig(scopeRoot);
+        if (definition.generation) {
+            if (definition.generation === 'projects-config-default') {
+                const config = await readOatConfig(scopeRoot);
+                return {
+                    definition,
+                    path: installedPath,
+                    status: config.projects?.root?.trim() ? 'present' : 'outdated',
+                    installedVersion: null,
+                    bundledVersion: null,
+                };
+            }
             return {
                 definition,
                 path: installedPath,
-                status: config.projects?.root?.trim() ? 'present' : 'outdated',
+                status: 'present',
                 installedVersion: null,
                 bundledVersion: null,
             };
         }
+        if (!definition.source) {
+            throw new Error(`Seeded pack asset ${definition.id} has no materialized source`);
+        }
+        const { realPath: bundledPath } = await validateRealPathWithinScope(join(assetsRoot, definition.source), assetsRoot);
+        const inventory = await inventoryStaticAsset(definition, realPath, bundledPath);
         return {
-            definition,
+            ...inventory,
             path: installedPath,
-            status: 'present',
-            installedVersion: null,
-            bundledVersion: null,
+            status: inventory.status === 'current' ? 'current' : 'present',
         };
     }
     if (!definition.source) {
         throw new Error(`Managed pack asset ${definition.id} has no materialized source`);
     }
-    const bundledPath = join(assetsRoot, definition.source);
+    const { realPath: bundledPath } = await validateRealPathWithinScope(join(assetsRoot, definition.source), assetsRoot);
     if (definition.kind === 'skill' || definition.kind === 'agent') {
         const inventory = await inventoryVersionedAsset(definition, realPath, bundledPath);
         return { ...inventory, path: installedPath };

package/dist/commands/tools/shared/project-tools-config.d.ts

@@ -1,6 +1,6 @@
 import { type OatConfig } from '../../../config/oat-config.js';
 import { type ScanToolsOptions } from './scan-tools.js';
-import type { ToolInfo } from './types.js';
+import type { PackName, ToolInfo } from './types.js';
 export interface ReconcileProjectToolsOptions {
     repoRoot: string;
     cwd: string;
@@ -12,5 +12,9 @@ export interface ProjectToolsConfigDependencies {
     readOatConfig: (repoRoot: string) => Promise<OatConfig>;
     writeOatConfig: (repoRoot: string, config: OatConfig) => Promise<void>;
 }
-export declare function reconcileProjectToolsConfig(options: ReconcileProjectToolsOptions, dependencies?: ProjectToolsConfigDependencies): Promise<'written' | 'unchanged'>;
+export interface ReconcileProjectToolsResult {
+    action: 'written' | 'unchanged';
+    adoptedPacks: PackName[];
+}
+export declare function reconcileProjectToolsConfig(options: ReconcileProjectToolsOptions, dependencies?: ProjectToolsConfigDependencies): Promise<ReconcileProjectToolsResult>;
 //# sourceMappingURL=project-tools-config.d.ts.map

package/dist/commands/tools/shared/project-tools-config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"project-tools-config.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/shared/project-tools-config.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,KAAK,SAAS,EAIf,MAAM,oBAAoB,CAAC;AAG5B,OAAO,EAAa,KAAK,gBAAgB,EAAE,MAAM,cAAc,CAAC;AAChE,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AAExC,MAAM,WAAW,4BAA4B;IAC3C,QAAQ,EAAE,MAAM,CAAC;IACjB,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,8BAA8B;IAC7C,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,SAAS,EAAE,CAAC,OAAO,EAAE,gBAAgB,KAAK,OAAO,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC9D,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;CACxE;AASD,wBAAsB,2BAA2B,CAC/C,OAAO,EAAE,4BAA4B,EACrC,YAAY,GAAE,8BAAoD,GACjE,OAAO,CAAC,SAAS,GAAG,WAAW,CAAC,CA2BlC"}
+{"version":3,"file":"project-tools-config.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/shared/project-tools-config.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,KAAK,SAAS,EAIf,MAAM,oBAAoB,CAAC;AAI5B,OAAO,EAAa,KAAK,gBAAgB,EAAE,MAAM,cAAc,CAAC;AAChE,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AAElD,MAAM,WAAW,4BAA4B;IAC3C,QAAQ,EAAE,MAAM,CAAC;IACjB,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,8BAA8B;IAC7C,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,SAAS,EAAE,CAAC,OAAO,EAAE,gBAAgB,KAAK,OAAO,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC9D,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;CACxE;AAED,MAAM,WAAW,2BAA2B;IAC1C,MAAM,EAAE,SAAS,GAAG,WAAW,CAAC;IAChC,YAAY,EAAE,QAAQ,EAAE,CAAC;CAC1B;AASD,wBAAsB,2BAA2B,CAC/C,OAAO,EAAE,4BAA4B,EACrC,YAAY,GAAE,8BAAoD,GACjE,OAAO,CAAC,2BAA2B,CAAC,CA6BtC"}

package/dist/commands/tools/shared/project-tools-config.js

@@ -1,5 +1,6 @@
 import { readOatConfig, writeOatConfig, } from '../../../config/oat-config.js';
 import { resolveAssetsRoot } from '../../../fs/assets.js';
+import { PACK_NAMES } from './pack-manifest.js';
 import { scanTools } from './scan-tools.js';
 const defaultDependencies = {
     resolveAssetsRoot,
@@ -16,18 +17,19 @@ export async function reconcileProjectToolsConfig(options, dependencies = defaul
     });
     const config = await dependencies.readOatConfig(options.repoRoot);
     const tools = { ...config.tools };
-    let changed = false;
+    const adopted = new Set();
     for (const tool of projectTools) {
         if (tool.scope === 'project' &&
             tool.pack !== 'custom' &&
             tools[tool.pack] !== true) {
             tools[tool.pack] = true;
-            changed = true;
+            adopted.add(tool.pack);
         }
     }
-    if (!changed) {
-        return 'unchanged';
+    const adoptedPacks = PACK_NAMES.filter((pack) => adopted.has(pack));
+    if (adoptedPacks.length === 0) {
+        return { action: 'unchanged', adoptedPacks };
     }
     await dependencies.writeOatConfig(options.repoRoot, { ...config, tools });
-    return 'written';
+    return { action: 'written', adoptedPacks };
 }

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":"AAgBA,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAK1C,OAAO,KAAK,EAAY,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AAKvE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EACL,KAAK,YAAY,EACjB,KAAK,YAAY,EACjB,KAAK,uBAAuB,EAE7B,MAAM,gBAAgB,CAAC;AAmBxB,wBAAgB,uBAAuB,CACrC,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM,EAAE,EAClB,OAAO,EAAE;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,SAAS,GAAG,MAAM,CAAA;CAAE,GAClD,MAAM,EAAE,CAaV;AAgCD,wBAAgB,wBAAwB,CACtC,YAAY,GAAE,uBAA6C,EAC3D,gBAAgB,GAAE,oBAA8C,GAC/D,OAAO,CA6LT;AAED;;;;GAIG;AACH,wBAAgB,+BAA+B,CAAC,MAAM,EAAE,YAAY,GAAG,OAAO,CAS7E;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":"AAgBA,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAK1C,OAAO,KAAK,EAAY,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AAKvE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EACL,KAAK,YAAY,EACjB,KAAK,YAAY,EACjB,KAAK,uBAAuB,EAE7B,MAAM,gBAAgB,CAAC;AAmBxB,wBAAgB,uBAAuB,CACrC,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM,EAAE,EAClB,OAAO,EAAE;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,SAAS,GAAG,MAAM,CAAA;CAAE,GAClD,MAAM,EAAE,CAaV;AAgCD,wBAAgB,wBAAwB,CACtC,YAAY,GAAE,uBAA6C,EAC3D,gBAAgB,GAAE,oBAA8C,GAC/D,OAAO,CA8MT;AAED;;;;GAIG;AACH,wBAAgB,+BAA+B,CAAC,MAAM,EAAE,YAAY,GAAG,OAAO,CAS7E;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

@@ -130,11 +130,12 @@ export function createToolsUpdateCommand(dependencies = defaultDependencies, syn
         const changedProjectScope = [...result.updated, ...result.current, ...result.newer].some(({ scope }) => scope === 'project') ||
             result.assetRefreshes.some(({ scope }) => scope === 'project') ||
             result.plans.some(({ scope }) => scope === 'project');
+        let adoptedPacks = [];
         if (assetsRoot &&
             result.notInstalled.length === 0 &&
             changedProjectScope) {
             const repoRoot = await resolveProjectRoot(context.cwd);
-            await reconcileProjectToolsConfig({
+            adoptedPacks = (await reconcileProjectToolsConfig({
                 repoRoot,
                 cwd: context.cwd,
                 home: context.home,
@@ -143,11 +144,16 @@ export function createToolsUpdateCommand(dependencies = defaultDependencies, syn
                 scanTools: dependencies.scanTools,
                 readOatConfig,
                 writeOatConfig,
-            });
+            })).adoptedPacks;
         }
         if (result.notInstalled.length > 0) {
             if (context.json) {
-                logger.json({ target: describeTarget(target), dryRun, result });
+                logger.json({
+                    target: describeTarget(target),
+                    dryRun,
+                    result,
+                    ...(adoptedPacks.length > 0 ? { adoptedPacks } : {}),
+                });
             }
             else {
                 logger.error(`Tool '${result.notInstalled[0]}' not found.`);
@@ -170,9 +176,17 @@ export function createToolsUpdateCommand(dependencies = defaultDependencies, syn
             }
         }
         if (context.json) {
-            logger.json({ target: describeTarget(target), dryRun, result });
+            logger.json({
+                target: describeTarget(target),
+                dryRun,
+                result,
+                ...(adoptedPacks.length > 0 ? { adoptedPacks } : {}),
+            });
             return;
         }
+        for (const pack of adoptedPacks) {
+            logger.info(`Adopted project tool pack: ${pack}`);
+        }
         if (result.updated.length > 0) {
             for (const tool of result.updated) {
                 logger.success(formatUpdatedToolMessage(tool, dryRun));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@open-agent-toolkit/cli",
-  "version": "0.2.45",
+  "version": "0.2.46",
   "private": false,
   "description": "Open Agent Toolkit CLI",
   "homepage": "https://github.com/voxmedia/open-agent-toolkit/tree/main/packages/cli",
@@ -34,7 +34,7 @@
     "ora": "^9.0.0",
     "yaml": "2.8.2",
     "zod": "^3.25.76",
-    "@open-agent-toolkit/control-plane": "0.2.45"
+    "@open-agent-toolkit/control-plane": "0.2.46"
   },
   "devDependencies": {
     "@types/node": "^22.10.0",