@open-agent-toolkit/cli 0.1.32 → 0.1.33

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

@@ -87,7 +87,7 @@ Tool-pack installation state also lives here as shared repo config:
 - `tools.utility`
 - `tools.workflows`
 
-Use `oat config get tools.<pack>` when you need an explicit installed-capability signal for workflows or troubleshooting.
+Use `oat config get tools.<pack>` when you need an explicit installed-capability signal for workflows or troubleshooting. PJM diagnostics use `tools.project-management`; disabled or unset repos report PJM as skipped instead of treating absent `.oat/repo/pjm/` files as drift.
 
 Workflow automation preferences are also visible through `oat config` and can be set at local, shared, or user scope. Notable review-loop keys:
 

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

@@ -53,7 +53,7 @@ Decisions are now file-per-record under `reference/decisions/` (created and inde
 
 `oat pjm init` is idempotent and non-destructive. Existing reference docs are skipped and left unchanged, so curated repo state is not overwritten on repeated runs.
 
-Run `oat pjm doctor` to check an existing surface: it reports missing canonical files, leftover template frontmatter, and legacy/loose/second-roadmap drift, and accepts `--json` for machine-readable output. The same checks also run under project-scope `oat doctor` when `.oat/repo` exists.
+Run `oat pjm doctor` to check an existing surface after the `project-management` pack is enabled: it reports missing canonical files, leftover template frontmatter, and legacy/loose/second-roadmap drift, and accepts `--json` for machine-readable output. When the pack is disabled or not configured, doctor reports PJM as disabled and skips drift checks. The same gated checks also run under project-scope `oat doctor`.
 
 Useful options:
 

package/assets/docs/reference/cli-reference.md

@@ -37,20 +37,20 @@ The first practical expansion path is to keep improving the existing owners: [Do
 
 ## Command Groups
 
-| Command group                                   | What it covers                                                                                                                                                                                                | Go deeper                                                                          |
-| ----------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------- |
-| `oat init`                                      | Bootstrap canonical OAT directories, sync config, optional hooks, and guided setup.                                                                                                                           | [CLI Bootstrap](../cli-utilities/bootstrap.md)                                     |
-| `oat tools ...`                                 | Install, inspect, update, and remove bundled OAT tool packs and assets.                                                                                                                                       | [Tool Packs](../cli-utilities/tool-packs.md)                                       |
-| `oat pjm ...`                                   | Initialize the two-layer repo-reference surface (`init`), run reference diagnostics (`doctor`), and migrate legacy layouts to `pjm/` + `reference/` (`migrate`) after installing the project-management pack. | [Install vs. initialize](../cli-utilities/tool-packs.md#install-vs-initialize)     |
-| `oat decision ...`                              | Create, index, and migrate file-per-record repo decisions under `reference/decisions/` (`init`, `new`, `regenerate-index`, `migrate`).                                                                        | [Config and Local State](../cli-utilities/config-and-local-state.md#oat-decision-) |
-| `oat backlog ...` / `oat local ...`             | File-backed backlog helpers, local path sync, and local-only operational support.                                                                                                                             | [Config and Local State](../cli-utilities/config-and-local-state.md)               |
-| `oat config ...` / `oat instructions ...`       | Config discovery, source-aware config dumps, supported mutations, and instruction-integrity helpers.                                                                                                          | [Config and Local State](../cli-utilities/config-and-local-state.md)               |
-| `oat state ...` / `oat index ...` / `internal`  | Repo dashboard refresh, repo indexing, validation helpers, and diagnostics.                                                                                                                                   | [Config and Local State](../cli-utilities/config-and-local-state.md)               |
-| `oat docs ...`                                  | Docs app bootstrap, migration, index generation, nav sync, and docs workflow entrypoints.                                                                                                                     | [Docs Tooling Commands](../docs-tooling/commands.md)                               |
-| `oat status` / `oat sync` / `oat providers ...` | Provider sync, drift inspection, provider configuration, and adoption behavior.                                                                                                                               | [Provider Sync](../provider-sync/index.md)                                         |
-| `oat project ...` / `oat cleanup ...`           | Project scaffolding, active-project status inspection, tracked-project listing, plan validation, archive creation, and project/artifact cleanup commands.                                                     | [Workflow & Projects](../workflows/projects/index.md)                              |
-| `oat review ...`                                | Review artifact discovery helpers, including latest-review resolution for project and ad-hoc review flows.                                                                                                    | [Reviews](../workflows/projects/reviews.md)                                        |
-| `oat repo ...`                                  | Repository-level workflows such as archive sync and PR-comment analysis.                                                                                                                                      | [Repository Analysis](../workflows/projects/repo-analysis.md)                      |
+| Command group                                   | What it covers                                                                                                                                                                                                             | Go deeper                                                                          |
+| ----------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------- |
+| `oat init`                                      | Bootstrap canonical OAT directories, sync config, optional hooks, and guided setup.                                                                                                                                        | [CLI Bootstrap](../cli-utilities/bootstrap.md)                                     |
+| `oat tools ...`                                 | Install, inspect, update, and remove bundled OAT tool packs and assets.                                                                                                                                                    | [Tool Packs](../cli-utilities/tool-packs.md)                                       |
+| `oat pjm ...`                                   | Initialize the two-layer repo-reference surface (`init`), run enabled-pack reference diagnostics (`doctor`), and migrate legacy layouts to `pjm/` + `reference/` (`migrate`) after installing the project-management pack. | [Install vs. initialize](../cli-utilities/tool-packs.md#install-vs-initialize)     |
+| `oat decision ...`                              | Create, index, and migrate file-per-record repo decisions under `reference/decisions/` (`init`, `new`, `regenerate-index`, `migrate`).                                                                                     | [Config and Local State](../cli-utilities/config-and-local-state.md#oat-decision-) |
+| `oat backlog ...` / `oat local ...`             | File-backed backlog helpers, local path sync, and local-only operational support.                                                                                                                                          | [Config and Local State](../cli-utilities/config-and-local-state.md)               |
+| `oat config ...` / `oat instructions ...`       | Config discovery, source-aware config dumps, supported mutations, and instruction-integrity helpers.                                                                                                                       | [Config and Local State](../cli-utilities/config-and-local-state.md)               |
+| `oat state ...` / `oat index ...` / `internal`  | Repo dashboard refresh, repo indexing, validation helpers, and diagnostics.                                                                                                                                                | [Config and Local State](../cli-utilities/config-and-local-state.md)               |
+| `oat docs ...`                                  | Docs app bootstrap, migration, index generation, nav sync, and docs workflow entrypoints.                                                                                                                                  | [Docs Tooling Commands](../docs-tooling/commands.md)                               |
+| `oat status` / `oat sync` / `oat providers ...` | Provider sync, drift inspection, provider configuration, and adoption behavior.                                                                                                                                            | [Provider Sync](../provider-sync/index.md)                                         |
+| `oat project ...` / `oat cleanup ...`           | Project scaffolding, active-project status inspection, tracked-project listing, plan validation, archive creation, and project/artifact cleanup commands.                                                                  | [Workflow & Projects](../workflows/projects/index.md)                              |
+| `oat review ...`                                | Review artifact discovery helpers, including latest-review resolution for project and ad-hoc review flows.                                                                                                                 | [Reviews](../workflows/projects/reviews.md)                                        |
+| `oat repo ...`                                  | Repository-level workflows such as archive sync and PR-comment analysis.                                                                                                                                                   | [Repository Analysis](../workflows/projects/repo-analysis.md)                      |
 
 Notable commands introduced in the current CLI surface:
 

package/assets/public-package-versions.json

@@ -1,6 +1,6 @@
 {
-  "cli": "0.1.32",
-  "docs-config": "0.1.32",
-  "docs-theme": "0.1.32",
-  "docs-transforms": "0.1.32"
+  "cli": "0.1.33",
+  "docs-config": "0.1.33",
+  "docs-theme": "0.1.33",
+  "docs-transforms": "0.1.33"
 }

package/assets/scripts/resolve-tracking.sh

@@ -100,6 +100,41 @@ resolve_root_commit_hash() {
   git rev-parse HEAD
 }
 
+is_agent_instructions_operation() {
+  local operation="${1:?Missing operation}"
+  [[ "$operation" == "agentInstructions" || "$operation" == "agentInstructionsApply" ]]
+}
+
+normalize_repo_relative_path() {
+  local path="${1:?Missing path}"
+
+  path="${path#./}"
+  if [[ "$path" == "$REPO_ROOT"/* ]]; then
+    path="${path#"$REPO_ROOT"/}"
+  fi
+
+  echo "$path"
+}
+
+artifact_path_is_tracked_and_present() {
+  local artifact_path="${1:?Missing artifact path}"
+  local relative_path absolute_path
+
+  relative_path="$(normalize_repo_relative_path "$artifact_path")"
+  absolute_path="${REPO_ROOT}/${relative_path}"
+
+  [[ -e "$absolute_path" ]] || return 1
+  git -C "$REPO_ROOT" ls-files --error-unmatch -- "$relative_path" >/dev/null 2>&1
+}
+
+remove_tracking_key() {
+  local operation="${1:?Missing operation}"
+  local existing="${2:?Missing existing tracking JSON}"
+
+  mkdir -p "$(dirname "$TRACKING_FILE")"
+  echo "$existing" | jq --arg op "$operation" 'del(.[$op])' > "$TRACKING_FILE"
+}
+
 cmd_init() {
   mkdir -p "$(dirname "$TRACKING_FILE")"
   if [[ ! -f "$TRACKING_FILE" ]] || ! jq empty "$TRACKING_FILE" 2>/dev/null; then
@@ -118,6 +153,16 @@ cmd_read() {
     return 0
   fi
 
+  if is_agent_instructions_operation "$operation"; then
+    local artifact_path
+    artifact_path="$(jq -r --arg op "$operation" '.[$op].artifactPath // empty' "$TRACKING_FILE")"
+    if [[ -n "$artifact_path" ]] && ! artifact_path_is_tracked_and_present "$artifact_path"; then
+      remove_tracking_key "$operation" "$(cat "$TRACKING_FILE")"
+      echo "{}"
+      return 0
+    fi
+  fi
+
   jq -r --arg op "$operation" '.[$op] // empty' "$TRACKING_FILE"
 }
 
@@ -172,6 +217,13 @@ cmd_write() {
     existing='{"version":1}'
   fi
 
+  if is_agent_instructions_operation "$operation" && [[ -n "$artifact_path" ]] && ! artifact_path_is_tracked_and_present "$artifact_path"; then
+    remove_tracking_key "$operation" "$existing"
+    echo "Info: skipped $operation tracking because artifactPath is missing or untracked: $artifact_path" >&2
+    echo "Updated $TRACKING_FILE [$operation]"
+    return 0
+  fi
+
   if [[ -n "$artifact_path" ]]; then
     echo "$existing" | jq \
       --arg op "$operation" \

package/dist/commands/doctor/index.d.ts

@@ -1,4 +1,6 @@
 import { type CommandContext, type GlobalOptions } from '../../app/command-context.js';
+import { type PjmDoctorOptions } from '../pjm/doctor.js';
+import { type OatConfig } from '../../config/oat-config.js';
 import { type Manifest } from '../../manifest/index.js';
 import type { ConcreteScope } from '../../shared/types.js';
 import { type DoctorCheck } from '../../ui/output.js';
@@ -16,7 +18,8 @@ interface DoctorDependencies {
     }>>;
     readFile: (path: string) => Promise<string>;
     resolveAssetsRoot: () => Promise<string>;
-    runPjmDoctorChecks: (repoRoot: string) => Promise<DoctorCheck[]>;
+    readOatConfig: (repoRoot: string) => Promise<OatConfig>;
+    runPjmDoctorChecks: (repoRoot: string, options?: PjmDoctorOptions) => Promise<DoctorCheck[]>;
     checkSkillVersions: (scopeRoot: string, assetsRoot: string, pathExists: (path: string) => Promise<boolean>) => Promise<SkillVersionReport>;
 }
 interface OutdatedSkillVersion {

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor/index.ts"],"names":[],"mappings":"AAWA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAW9B,OAAO,EAAgB,KAAK,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAM9D,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AACnD,OAAO,EAAE,KAAK,WAAW,EAAuB,MAAM,YAAY,CAAC;AACnE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,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,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IAC/C,YAAY,EAAE,CAAC,YAAY,EAAE,MAAM,KAAK,OAAO,CAAC,QAAQ,CAAC,CAAC;IAC1D,mBAAmB,EAAE,CAAC,SAAS,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IAC7D,cAAc,EAAE,CACd,SAAS,EAAE,MAAM,KACd,OAAO,CACV,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,OAAO,CAAC;QAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAA;KAAE,CAAC,CACnE,CAAC;IACF,QAAQ,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IAC5C,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,kBAAkB,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,WAAW,EAAE,CAAC,CAAC;IACjE,kBAAkB,EAAE,CAClB,SAAS,EAAE,MAAM,EACjB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,KAC3C,OAAO,CAAC,kBAAkB,CAAC,CAAC;CAClC;AAED,UAAU,oBAAoB;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED,UAAU,kBAAkB;IAC1B,mBAAmB,EAAE,MAAM,CAAC;IAC5B,0BAA0B,EAAE,MAAM,CAAC;IACnC,cAAc,EAAE,oBAAoB,EAAE,CAAC;CACxC;AA8aD,wBAAgB,mBAAmB,CACjC,SAAS,GAAE,OAAO,CAAC,kBAAkB,CAAM,GAC1C,OAAO,CAcT"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor/index.ts"],"names":[],"mappings":"AAWA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EAGL,KAAK,gBAAgB,EACtB,MAAM,sBAAsB,CAAC;AAM9B,OAAO,EAAiB,KAAK,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAInE,OAAO,EAAgB,KAAK,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAM9D,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AACnD,OAAO,EAAE,KAAK,WAAW,EAAuB,MAAM,YAAY,CAAC;AACnE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,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,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IAC/C,YAAY,EAAE,CAAC,YAAY,EAAE,MAAM,KAAK,OAAO,CAAC,QAAQ,CAAC,CAAC;IAC1D,mBAAmB,EAAE,CAAC,SAAS,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IAC7D,cAAc,EAAE,CACd,SAAS,EAAE,MAAM,KACd,OAAO,CACV,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,OAAO,CAAC;QAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAA;KAAE,CAAC,CACnE,CAAC;IACF,QAAQ,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IAC5C,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,kBAAkB,EAAE,CAClB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,gBAAgB,KACvB,OAAO,CAAC,WAAW,EAAE,CAAC,CAAC;IAC5B,kBAAkB,EAAE,CAClB,SAAS,EAAE,MAAM,EACjB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,KAC3C,OAAO,CAAC,kBAAkB,CAAC,CAAC;CAClC;AAED,UAAU,oBAAoB;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED,UAAU,kBAAkB;IAC1B,mBAAmB,EAAE,MAAM,CAAC;IAC5B,0BAA0B,EAAE,MAAM,CAAC;IACnC,cAAc,EAAE,oBAAoB,EAAE,CAAC;CACxC;AAsbD,wBAAgB,mBAAmB,CACjC,SAAS,GAAE,OAAO,CAAC,kBAAkB,CAAM,GAC1C,OAAO,CAcT"}

package/dist/commands/doctor/index.js

@@ -3,9 +3,10 @@ import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { buildCommandContext, } from '../../app/command-context.js';
 import { compareVersions } from '../init/tools/shared/version.js';
-import { runPjmDoctorChecks } from '../pjm/doctor.js';
+import { createPjmDisabledCheck, runPjmDoctorChecks, } from '../pjm/doctor.js';
 import { getSkillVersion } from '../shared/frontmatter.js';
 import { readGlobalOptions, resolveConcreteScopes, } from '../shared/shared.utils.js';
+import { readOatConfig } from '../../config/oat-config.js';
 import { resolveAssetsRoot } from '../../fs/assets.js';
 import { resolveProjectRoot, resolveScopeRoot } from '../../fs/paths.js';
 import TOML from '@iarna/toml';
@@ -126,6 +127,7 @@ function createDependencies() {
         checkProviders: checkProvidersDefault,
         readFile: async (path) => readFile(path, 'utf8'),
         resolveAssetsRoot,
+        readOatConfig,
         runPjmDoctorChecks,
         // Default binding remains self-contained, but still honors the caller-
         // provided pathExists dependency from runChecksForScope when available.
@@ -342,8 +344,15 @@ async function runChecksForScope(scope, scopeRoot, dependencies) {
             }
         }
         const repoReferenceRoot = join(scopeRoot, '.oat', 'repo');
-        if (await dependencies.pathExists(repoReferenceRoot)) {
-            checks.push(...(await dependencies.runPjmDoctorChecks(repoReferenceRoot)));
+        const config = await dependencies.readOatConfig(scopeRoot);
+        const projectManagementEnabled = config.tools?.['project-management'] === true;
+        if (projectManagementEnabled) {
+            checks.push(...(await dependencies.runPjmDoctorChecks(repoReferenceRoot, {
+                projectManagementEnabled: true,
+            })));
+        }
+        else if (await dependencies.pathExists(repoReferenceRoot)) {
+            checks.push(createPjmDisabledCheck());
         }
     }
     return checks;

package/dist/commands/pjm/doctor.d.ts

@@ -1,3 +1,7 @@
 import type { DoctorCheck } from '../../ui/output.js';
-export declare function runPjmDoctorChecks(repoRoot: string): Promise<DoctorCheck[]>;
+export interface PjmDoctorOptions {
+    projectManagementEnabled?: boolean;
+}
+export declare function createPjmDisabledCheck(): DoctorCheck;
+export declare function runPjmDoctorChecks(repoRoot: string, options?: PjmDoctorOptions): Promise<DoctorCheck[]>;
 //# sourceMappingURL=doctor.d.ts.map

package/dist/commands/pjm/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../src/commands/pjm/doctor.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AA0I9C,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,WAAW,EAAE,CAAC,CAqJxB"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../src/commands/pjm/doctor.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AA0I9C,MAAM,WAAW,gBAAgB;IAC/B,wBAAwB,CAAC,EAAE,OAAO,CAAC;CACpC;AAED,wBAAgB,sBAAsB,IAAI,WAAW,CAQpD;AAED,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,WAAW,EAAE,CAAC,CAyJxB"}

package/dist/commands/pjm/doctor.js

@@ -114,7 +114,19 @@ function checkStatus(missing) {
 function warnStatus(items) {
     return items.length === 0 ? 'pass' : 'warn';
 }
-export async function runPjmDoctorChecks(repoRoot) {
+export function createPjmDisabledCheck() {
+    return {
+        name: 'pjm:disabled',
+        description: 'Project-management pack enablement',
+        status: 'pass',
+        message: 'Project-management pack is disabled; PJM checks skipped.',
+        fix: 'Run `oat init tools project-management` to install and enable PJM checks.',
+    };
+}
+export async function runPjmDoctorChecks(repoRoot, options = {}) {
+    if (options.projectManagementEnabled === false) {
+        return [createPjmDisabledCheck()];
+    }
     const checks = [];
     const missingCanonical = [];
     for (const relativePath of CANONICAL_REPO_REFERENCE_PATHS) {

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/pjm/index.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,mBAAmB,EAAuB,MAAM,sBAAsB,CAAC;AAEhF,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AACnD,OAAO,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAC/C,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAC;AAE/C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAAE,kBAAkB,EAAE,MAAM,UAAU,CAAC;AAC9C,OAAO,EAAE,uBAAuB,EAAE,MAAM,QAAQ,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAC;AAiBnE,UAAU,sBAAsB;IAC9B,mBAAmB,EAAE,OAAO,mBAAmB,CAAC;IAChD,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,aAAa,EAAE,OAAO,aAAa,CAAC;IACpC,uBAAuB,EAAE,OAAO,uBAAuB,CAAC;IACxD,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,cAAc,EAAE,OAAO,cAAc,CAAC;IACtC,sBAAsB,EAAE,OAAO,sBAAsB,CAAC;CACvD;AA6FD,wBAAgB,gBAAgB,CAC9B,SAAS,GAAE,OAAO,CAAC,sBAAsB,CAAM,GAC9C,OAAO,CAkJT"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/pjm/index.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,mBAAmB,EAAuB,MAAM,sBAAsB,CAAC;AAEhF,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AACnD,OAAO,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAC/C,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAC;AAE/C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAAE,kBAAkB,EAAE,MAAM,UAAU,CAAC;AAC9C,OAAO,EAAE,uBAAuB,EAAE,MAAM,QAAQ,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAC;AAiBnE,UAAU,sBAAsB;IAC9B,mBAAmB,EAAE,OAAO,mBAAmB,CAAC;IAChD,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,aAAa,EAAE,OAAO,aAAa,CAAC;IACpC,uBAAuB,EAAE,OAAO,uBAAuB,CAAC;IACxD,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,cAAc,EAAE,OAAO,cAAc,CAAC;IACtC,sBAAsB,EAAE,OAAO,sBAAsB,CAAC;CACvD;AA6FD,wBAAgB,gBAAgB,CAC9B,SAAS,GAAE,OAAO,CAAC,sBAAsB,CAAM,GAC9C,OAAO,CAsJT"}

package/dist/commands/pjm/index.js

@@ -120,14 +120,17 @@ export function createPjmCommand(overrides = {}) {
     });
     cmd
         .command('doctor')
-        .description('Run PJM repo reference diagnostics')
+        .description('Run PJM repo reference diagnostics when enabled')
         .option('--repo-root <path>', 'PJM repo reference root directory (defaults to .oat/repo)')
         .action(async (options, command) => {
         const context = dependencies.buildCommandContext(readGlobalOptions(command));
         try {
             const projectRoot = await dependencies.resolveProjectRoot(context.cwd);
             const repoRoot = await resolveRepoRoot(context, projectRoot, options.repoRoot);
-            const checks = await dependencies.runPjmDoctorChecks(repoRoot);
+            const config = await dependencies.readOatConfig(projectRoot);
+            const checks = await dependencies.runPjmDoctorChecks(repoRoot, {
+                projectManagementEnabled: config.tools?.['project-management'] === true,
+            });
             const status = doctorStatus(checks);
             if (context.json) {
                 context.logger.json({ status, repoRoot, checks });

package/dist/commands/sync/apply.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"apply.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/apply.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAE3D,OAAO,KAAK,EACV,aAAa,EACb,uBAAuB,EAExB,MAAM,cAAc,CAAC;AAgEtB,wBAAsB,YAAY,CAChC,OAAO,EAAE,cAAc,EACvB,UAAU,EAAE,aAAa,EAAE,EAC3B,YAAY,EAAE,uBAAuB,GACpC,OAAO,CAAC,IAAI,CAAC,CAwEf"}
+{"version":3,"file":"apply.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/apply.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,KAAK,EACV,aAAa,EACb,uBAAuB,EAExB,MAAM,cAAc,CAAC;AAgEtB,wBAAsB,YAAY,CAChC,OAAO,EAAE,cAAc,EACvB,UAAU,EAAE,aAAa,EAAE,EAC3B,YAAY,EAAE,uBAAuB,GACpC,OAAO,CAAC,IAAI,CAAC,CA8Ef"}

package/dist/commands/sync/apply.js

@@ -1,3 +1,4 @@
+import { OAT_VERSION } from '../../shared/oat-version.js';
 import { countPlannedOperations } from './sync.utils.js';
 function countSkippedEntries(scopePlans) {
     return scopePlans.reduce((total, scopePlan) => {
@@ -45,10 +46,13 @@ export async function runSyncApply(context, scopePlans, dependencies) {
     for (const scopePlan of scopePlans) {
         const hasSyncEntries = scopePlan.plan.entries.length > 0 || scopePlan.plan.removals.length > 0;
         const hasCodexPlannedOperations = scopePlan.codexExtensionPlan?.operations.some((operation) => operation.action !== 'skip') ?? false;
-        if (!hasSyncEntries && !hasCodexPlannedOperations) {
+        const shouldRefreshManifestVersion = scopePlan.manifest.oatVersion !== OAT_VERSION;
+        if (!hasSyncEntries &&
+            !hasCodexPlannedOperations &&
+            !shouldRefreshManifestVersion) {
             continue;
         }
-        if (hasSyncEntries) {
+        if (hasSyncEntries || shouldRefreshManifestVersion) {
             const result = await dependencies.executeSyncPlan(scopePlan.plan, scopePlan.manifest, scopePlan.manifestPath);
             applied += result.applied;
             failed += result.failed;

package/dist/manifest/manager.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manager.d.ts","sourceRoot":"","sources":["../../src/manifest/manager.ts"],"names":[],"mappings":"AAOA,OAAO,EACL,KAAK,QAAQ,EACb,KAAK,aAAa,EAEnB,MAAM,kBAAkB,CAAC;AAa1B,wBAAgB,mBAAmB,IAAI,QAAQ,CAO9C;AAED,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CA6C1E;AAED,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAQf;AAED,wBAAgB,SAAS,CACvB,QAAQ,EAAE,QAAQ,EAClB,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,aAAa,GAAG,SAAS,CAK3B;AAED,wBAAgB,QAAQ,CAAC,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,aAAa,GAAG,QAAQ,CAc3E;AAED,wBAAgB,WAAW,CACzB,QAAQ,EAAE,QAAQ,EAClB,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,QAAQ,CAeV"}
+{"version":3,"file":"manager.d.ts","sourceRoot":"","sources":["../../src/manifest/manager.ts"],"names":[],"mappings":"AAOA,OAAO,EACL,KAAK,QAAQ,EACb,KAAK,aAAa,EAEnB,MAAM,kBAAkB,CAAC;AAa1B,wBAAgB,mBAAmB,IAAI,QAAQ,CAO9C;AAED,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CA6C1E;AAED,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAWf;AAED,wBAAgB,SAAS,CACvB,QAAQ,EAAE,QAAQ,EAClB,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,aAAa,GAAG,SAAS,CAK3B;AAED,wBAAgB,QAAQ,CAAC,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,aAAa,GAAG,QAAQ,CAc3E;AAED,wBAAgB,WAAW,CACzB,QAAQ,EAAE,QAAQ,EAClB,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,QAAQ,CAeV"}

package/dist/manifest/manager.js

@@ -54,7 +54,10 @@ export async function loadManifest(manifestPath) {
     }
 }
 export async function saveManifest(manifestPath, manifest) {
-    const validated = ManifestSchema.parse(manifest);
+    const validated = ManifestSchema.parse({
+        ...manifest,
+        oatVersion: OAT_VERSION,
+    });
     const dir = dirname(manifestPath);
     const tempPath = `${manifestPath}.${randomUUID()}.tmp`;
     await mkdir(dir, { recursive: true });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@open-agent-toolkit/cli",
-  "version": "0.1.32",
+  "version": "0.1.33",
   "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": "0.1.32"
+    "@open-agent-toolkit/control-plane": "0.1.33"
   },
   "devDependencies": {
     "@types/node": "^22.10.0",