ctxr-cli 0.4.0 → 0.4.1

package/dist/core/hooks.js.map

@@ -1 +1 @@
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package/dist/core/json-config-merge.d.ts

@@ -1,13 +1,37 @@
+/** A Claude Code hook-config entry, e.g. one `hooks.PreToolUse[]` element. */
+export interface HookMatcherEntry {
+    matcher: string;
+    hooks: readonly {
+        type: string;
+        command: string;
+        [key: string]: unknown;
+    }[];
+    [key: string]: unknown;
+}
+export type MergeListValue = readonly string[] | readonly HookMatcherEntry[];
+export type MergePatch = Readonly<Record<string, Readonly<Record<string, MergeListValue>>>>;
+export type RemovePatch = Readonly<Record<string, Readonly<Record<string, readonly string[]>>>>;
 /**
  * A structured-JSON counterpart to the marker-fenced text writer (context-
  * store spec's generated-region convention): JSON has no comment syntax to
  * carry a fence marker in, so a harness permission config (task 8.4) is
- * merged by array union instead — contexture's own rules are appended only
+ * merged by list union instead — contexture's own rules are appended only
  * if not already present, so a hand-added rule survives untouched and a
  * second run with the same rule set is a true no-op (byte-identical file,
  * no write at all).
+ *
+ * Two list shapes are supported: a string list (permission rules), unioned
+ * and, when `options.remove` names entries a previous release emitted, first
+ * pruned of exact matches (never a predicate sweep — that would also catch a
+ * hand-added rule of the same shape); and a hook-matcher-entry list, upserted
+ * by `mergeHookEntries` above. A list key that empties out because removal
+ * took its last entry is dropped entirely, so a migrated store converges to
+ * the same shape as a freshly generated one; a list key that was already an
+ * empty array on disk, untouched by removal, is left as `[]`.
  */
-export declare function mergeJsonArrayLists(filePath: string, patch: Readonly<Record<string, Readonly<Record<string, readonly string[]>>>>): Promise<{
+export declare function mergeJsonArrayLists(filePath: string, patch: MergePatch, options?: {
+    remove?: RemovePatch;
+}): Promise<{
     changed: boolean;
 }>;
 //# sourceMappingURL=json-config-merge.d.ts.map

package/dist/core/json-config-merge.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"json-config-merge.d.ts","sourceRoot":"","sources":["../../src/core/json-config-merge.ts"],"names":[],"mappings":"AAKA,8EAA8E;AAC9E,MAAM,WAAW,gBAAgB;IAC/B,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,SAAS;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;QAAC,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAA;KAAE,EAAE,CAAC;IAC5E,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;CACxB;AAED,MAAM,MAAM,cAAc,GAAG,SAAS,MAAM,EAAE,GAAG,SAAS,gBAAgB,EAAE,CAAC;AAC7E,MAAM,MAAM,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC;AAC5F,MAAM,MAAM,WAAW,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,SAAS,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;AAuBhG;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,UAAU,EACjB,OAAO,CAAC,EAAE;IAAE,MAAM,CAAC,EAAE,WAAW,CAAA;CAAE,GACjC,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CA4D/B"}

package/dist/core/json-config-merge.js

@@ -2,16 +2,44 @@ import { readFile } from 'node:fs/promises';
 import { mkdir } from 'node:fs/promises';
 import path from 'node:path';
 import { writeFileAtomic } from './fs/atomic.js';
+function isHookEntryList(value) {
+    return value.length > 0 && typeof value[0] === 'object' && value[0] !== null;
+}
+/**
+ * Upserts each incoming hook-matcher entry into the existing list, matched
+ * by its own `hooks[0].command` (the path to contexture's generated
+ * script): replaced in place when found, so regeneration is idempotent,
+ * appended otherwise. Any entry with a different command — an operator's
+ * own hook — is left untouched.
+ */
+function mergeHookEntries(existing, incoming) {
+    let result = [...existing];
+    for (const entry of incoming) {
+        const command = entry.hooks[0]?.command;
+        const index = result.findIndex((candidate) => candidate.hooks?.[0]?.command === command);
+        result = index === -1 ? [...result, entry] : result.map((candidate, i) => (i === index ? entry : candidate));
+    }
+    return result;
+}
 /**
  * A structured-JSON counterpart to the marker-fenced text writer (context-
  * store spec's generated-region convention): JSON has no comment syntax to
  * carry a fence marker in, so a harness permission config (task 8.4) is
- * merged by array union instead — contexture's own rules are appended only
+ * merged by list union instead — contexture's own rules are appended only
  * if not already present, so a hand-added rule survives untouched and a
  * second run with the same rule set is a true no-op (byte-identical file,
  * no write at all).
+ *
+ * Two list shapes are supported: a string list (permission rules), unioned
+ * and, when `options.remove` names entries a previous release emitted, first
+ * pruned of exact matches (never a predicate sweep — that would also catch a
+ * hand-added rule of the same shape); and a hook-matcher-entry list, upserted
+ * by `mergeHookEntries` above. A list key that empties out because removal
+ * took its last entry is dropped entirely, so a migrated store converges to
+ * the same shape as a freshly generated one; a list key that was already an
+ * empty array on disk, untouched by removal, is left as `[]`.
  */
-export async function mergeJsonArrayLists(filePath, patch) {
+export async function mergeJsonArrayLists(filePath, patch, options) {
     let existing = {};
     try {
         existing = JSON.parse(await readFile(filePath, 'utf8'));
@@ -22,13 +50,39 @@ export async function mergeJsonArrayLists(filePath, patch) {
     }
     const before = JSON.stringify(existing);
     const merged = { ...existing };
-    for (const [topKey, sections] of Object.entries(patch)) {
+    const removePatch = options?.remove ?? {};
+    const topKeys = new Set([...Object.keys(patch), ...Object.keys(removePatch)]);
+    for (const topKey of topKeys) {
+        const sections = patch[topKey] ?? {};
+        const removeSections = removePatch[topKey] ?? {};
         const existingTop = merged[topKey] ?? {};
         const mergedTop = { ...existingTop };
-        for (const [listKey, newValues] of Object.entries(sections)) {
-            const existingList = Array.isArray(existingTop[listKey]) ? existingTop[listKey] : [];
-            const additions = newValues.filter((v) => !existingList.includes(v));
-            mergedTop[listKey] = [...existingList, ...additions];
+        const listKeys = new Set([...Object.keys(sections), ...Object.keys(removeSections)]);
+        for (const listKey of listKeys) {
+            const newValues = sections[listKey] ?? [];
+            const toRemove = removeSections[listKey] ?? [];
+            const existingRaw = existingTop[listKey];
+            const existingListPresent = Array.isArray(existingRaw);
+            const existingList = existingListPresent ? existingRaw : [];
+            if (isHookEntryList(newValues) || (existingList.length > 0 && typeof existingList[0] === 'object')) {
+                mergedTop[listKey] = mergeHookEntries(existingList, newValues);
+                continue;
+            }
+            const existingStrings = existingList;
+            const removedCount = existingStrings.filter((v) => toRemove.includes(v)).length;
+            const afterRemoval = existingStrings.filter((v) => !toRemove.includes(v));
+            const additions = newValues.filter((v) => !afterRemoval.includes(v));
+            const result = [...afterRemoval, ...additions];
+            if (result.length === 0) {
+                if (removedCount > 0) {
+                    delete mergedTop[listKey];
+                }
+                else if (existingListPresent && existingStrings.length === 0) {
+                    mergedTop[listKey] = [];
+                }
+                continue;
+            }
+            mergedTop[listKey] = result;
         }
         merged[topKey] = mergedTop;
     }

package/dist/core/json-config-merge.js.map

@@ -1 +1 @@
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package/dist/core/migrations/registry.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/core/migrations/registry.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAE5C,gHAAgH;AAChH,eAAO,MAAM,UAAU,EAAE,SAAS,SAAS,EAAqC,CAAC;AAEjF,qHAAqH;AACrH,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG,SAAS,EAAE,CAElE"}
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/core/migrations/registry.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAE5C,gHAAgH;AAChH,eAAO,MAAM,UAAU,EAAE,SAAS,SAAS,EAAoE,CAAC;AAEhH,qHAAqH;AACrH,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG,SAAS,EAAE,CAElE"}

package/dist/core/migrations/registry.js

@@ -1,6 +1,7 @@
+import { renameProceduresPathMigration } from './rename-procedures-path.js';
 import { renameVisibilityFieldMigration } from './rename-visibility-field.js';
 /** Every migration contexture ships, in ascending fromVersion order. Later phases append here, nothing else. */
-export const MIGRATIONS = [renameVisibilityFieldMigration];
+export const MIGRATIONS = [renameVisibilityFieldMigration, renameProceduresPathMigration];
 /** Every migration a store currently at `fromVersion` still needs to reach the CLI's supported version, in order. */
 export function pendingMigrations(fromVersion) {
     return MIGRATIONS.filter((m) => m.fromVersion >= fromVersion).slice().sort((a, b) => a.fromVersion - b.fromVersion);

package/dist/core/migrations/registry.js.map

@@ -1 +1 @@
-{"version":3,"file":"registry.js","sourceRoot":"","sources":["../../../src/core/migrations/registry.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,8BAA8B,EAAE,MAAM,8BAA8B,CAAC;AAG9E,gHAAgH;AAChH,MAAM,CAAC,MAAM,UAAU,GAAyB,CAAC,8BAA8B,CAAC,CAAC;AAEjF,qHAAqH;AACrH,MAAM,UAAU,iBAAiB,CAAC,WAAmB;IACnD,OAAO,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,IAAI,WAAW,CAAC,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC;AACtH,CAAC"}
+{"version":3,"file":"registry.js","sourceRoot":"","sources":["../../../src/core/migrations/registry.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,6BAA6B,EAAE,MAAM,6BAA6B,CAAC;AAC5E,OAAO,EAAE,8BAA8B,EAAE,MAAM,8BAA8B,CAAC;AAG9E,gHAAgH;AAChH,MAAM,CAAC,MAAM,UAAU,GAAyB,CAAC,8BAA8B,EAAE,6BAA6B,CAAC,CAAC;AAEhH,qHAAqH;AACrH,MAAM,UAAU,iBAAiB,CAAC,WAAmB;IACnD,OAAO,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,IAAI,WAAW,CAAC,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC;AACtH,CAAC"}

package/dist/core/migrations/rename-procedures-path.d.ts

@@ -0,0 +1,17 @@
+import type { Migration } from './types.js';
+/**
+ * rename-procedures-to-skills (design.md D2): a single-delta migration —
+ * unlike the visibility-field rename, no note frontmatter is touched, since
+ * only the config key's spelling changes, never any store file's location
+ * (DEFAULT_SKILLS_PATH is already DEFAULT_PROCEDURES_PATH's old value).
+ *
+ * Pending-ness is `store.config.schema_version < 3`, NOT the presence or
+ * absence of `store.config.harness.skills_path` — that field is populated
+ * by HarnessSchema's fallback transform even on an unmigrated v2 store (so
+ * every command keeps working before `ctxr migrate` runs), which means its
+ * presence can never distinguish "already migrated" from "not yet
+ * migrated." `schema_version` is the one signal the fallback doesn't mask,
+ * and this migration is the only thing that ever sets it to 3.
+ */
+export declare const renameProceduresPathMigration: Migration;
+//# sourceMappingURL=rename-procedures-path.d.ts.map

package/dist/core/migrations/rename-procedures-path.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"rename-procedures-path.d.ts","sourceRoot":"","sources":["../../../src/core/migrations/rename-procedures-path.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,SAAS,EAAkB,MAAM,YAAY,CAAC;AAO5D;;;;;;;;;;;;;GAaG;AACH,eAAO,MAAM,6BAA6B,EAAE,SAwB3C,CAAC"}

package/dist/core/migrations/rename-procedures-path.js

@@ -0,0 +1,45 @@
+import path from 'node:path';
+import { readConfig } from '../../config/load.js';
+import { renderStoreConfig } from '../../config/render.js';
+import { writeFileAtomic } from '../fs/atomic.js';
+const CONFIG_DELTA = {
+    path: 'contexture.yaml',
+    description: 'rename harness.procedures_path to harness.skills_path and set schema_version to 3',
+};
+/**
+ * rename-procedures-to-skills (design.md D2): a single-delta migration —
+ * unlike the visibility-field rename, no note frontmatter is touched, since
+ * only the config key's spelling changes, never any store file's location
+ * (DEFAULT_SKILLS_PATH is already DEFAULT_PROCEDURES_PATH's old value).
+ *
+ * Pending-ness is `store.config.schema_version < 3`, NOT the presence or
+ * absence of `store.config.harness.skills_path` — that field is populated
+ * by HarnessSchema's fallback transform even on an unmigrated v2 store (so
+ * every command keeps working before `ctxr migrate` runs), which means its
+ * presence can never distinguish "already migrated" from "not yet
+ * migrated." `schema_version` is the one signal the fallback doesn't mask,
+ * and this migration is the only thing that ever sets it to 3.
+ */
+export const renameProceduresPathMigration = {
+    id: '0003-rename-procedures-path-to-skills-path',
+    fromVersion: 2,
+    toVersion: 3,
+    description: 'Rename the harness.procedures_path config key to harness.skills_path, and bump schema_version to 3.',
+    async plan(store) {
+        return store.config.schema_version < 3 ? [CONFIG_DELTA] : [];
+    },
+    async apply(store) {
+        if (store.config.schema_version >= 3)
+            return [];
+        const configPath = path.join(store.root, 'contexture.yaml');
+        // readConfig() already resolves harness.skills_path via HarnessSchema's
+        // fallback (from procedures_path if that's all the file has), so
+        // currentConfig.harness carries no procedures_path key at all —
+        // rendering it below writes only skills_path to disk.
+        const currentConfig = await readConfig(store.root);
+        const nextConfig = { ...currentConfig, schema_version: 3 };
+        await writeFileAtomic(configPath, renderStoreConfig(nextConfig));
+        return [CONFIG_DELTA];
+    },
+};
+//# sourceMappingURL=rename-procedures-path.js.map

package/dist/core/migrations/rename-procedures-path.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"rename-procedures-path.js","sourceRoot":"","sources":["../../../src/core/migrations/rename-procedures-path.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,UAAU,EAAE,MAAM,sBAAsB,CAAC;AAClD,OAAO,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAC;AAC3D,OAAO,EAAE,eAAe,EAAE,MAAM,iBAAiB,CAAC;AAIlD,MAAM,YAAY,GAAmB;IACnC,IAAI,EAAE,iBAAiB;IACvB,WAAW,EAAE,mFAAmF;CACjG,CAAC;AAEF;;;;;;;;;;;;;GAaG;AACH,MAAM,CAAC,MAAM,6BAA6B,GAAc;IACtD,EAAE,EAAE,4CAA4C;IAChD,WAAW,EAAE,CAAC;IACd,SAAS,EAAE,CAAC;IACZ,WAAW,EAAE,qGAAqG;IAElH,KAAK,CAAC,IAAI,CAAC,KAAK;QACd,OAAO,KAAK,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IAC/D,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,KAAK;QACf,IAAI,KAAK,CAAC,MAAM,CAAC,cAAc,IAAI,CAAC;YAAE,OAAO,EAAE,CAAC;QAEhD,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,iBAAiB,CAAC,CAAC;QAC5D,wEAAwE;QACxE,iEAAiE;QACjE,gEAAgE;QAChE,sDAAsD;QACtD,MAAM,aAAa,GAAG,MAAM,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACnD,MAAM,UAAU,GAAG,EAAE,GAAG,aAAa,EAAE,cAAc,EAAE,CAAC,EAAE,CAAC;QAC3D,MAAM,eAAe,CAAC,UAAU,EAAE,iBAAiB,CAAC,UAAU,CAAC,CAAC,CAAC;QAEjE,OAAO,CAAC,YAAY,CAAC,CAAC;IACxB,CAAC;CACF,CAAC"}

package/dist/core/notes/list.js

@@ -6,8 +6,8 @@ import { parseNote } from './parse.js';
 const ALWAYS_SKIP_DIRS = new Set(['.git', '.githooks', '.queue']);
 /**
  * Filenames intrinsic to contexture itself, never user content — same
- * status as ALWAYS_SKIP_DIRS. AGENTS.md is a CLI-generated procedure
- * document (task 4.5), not a note, but only the one `agentsMdPath` ever
+ * status as ALWAYS_SKIP_DIRS. AGENTS.md is a CLI-generated document
+ * (task 4.5), not a note, but only the one `agentsMdPath` ever
  * generates: the store root's own `AGENTS.md` (`agents-doc.ts` hardcodes
  * `path.join(root, 'AGENTS.md')`, never a nested path). A same-named file
  * anywhere else is ordinary content an operator happened to name AGENTS.md
@@ -42,7 +42,7 @@ export function excludedPrefixesFor(config) {
         config.session.worktrees_path,
         config.catalog.path,
         // Tool-owned instruction docs (skills, conventions) are never notes, wherever they live.
-        config.harness.procedures_path,
+        config.harness.skills_path,
         config.harness.conventions_path,
     ];
 }

package/dist/core/notes/list.js.map

@@ -1 +1 @@
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package/dist/core/reconcile.js

@@ -3,7 +3,7 @@ import { agentsMdPath, buildAgentsCanonicalSection, buildAgentsCaptureSection, b
 import { removeFencedRegionFromFile, upsertFencedRegionInFile } from './fs/fenced-region.js';
 import { configureHooksPath, installHooks } from './hooks.js';
 import { commentFence, DERIVED_GITIGNORE_FENCE, htmlCommentFence } from './markers.js';
-import { syncShippedSkills } from './procedures.js';
+import { syncShippedSkills } from './skills.js';
 export const WORKTREES_GITIGNORE_FENCE = commentFence('worktrees');
 /**
  * remove-agent-identity: AGENTS.md's old "Agent identity" section is an
@@ -33,7 +33,7 @@ export async function reconcileStore(env, root, config) {
     note('.gitignore', (await upsertFencedRegionInFile(gitignorePath, DERIVED_GITIGNORE_FENCE, config.derived.paths)).changed);
     note('.gitignore', (await upsertFencedRegionInFile(gitignorePath, WORKTREES_GITIGNORE_FENCE, [config.session.worktrees_path])).changed);
     // Files the generated sections index (skills) must be current BEFORE the
-    // sections are rendered — the procedure index is a disk scan.
+    // sections are rendered — the skill index is a disk scan.
     changed.push(...(await syncShippedSkills(root, config)));
     let agentsChanged = false;
     for (const build of [

package/dist/core/reconcile.js.map

@@ -1 +1 @@
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package/dist/core/{procedures.d.ts → skills.d.ts}

@@ -2,10 +2,10 @@ import type { StoreConfig, TaxonomyLayerConfig } from '../config/schema.js';
 import { type ScannedDoc } from './conventions.js';
 /**
  * harness-portability spec (task 8.6, revised by entry-doc-generation D5,
- * expanded by owned-skills-expansion): reusable store procedures ship as
- * contexture-OWNED skills. The canonical content is this module (versioned
+ * expanded by owned-skills-expansion): reusable store skills ship as
+ * contexture-OWNED files. The canonical content is this module (versioned
  * with the package); a store carries a full copy at
- * `<procedures_path>/ctxr-<slug>/SKILL.md` — written by `ctxr init`,
+ * `<skills_path>/ctxr-<slug>/SKILL.md` — written by `ctxr init`,
  * refreshed by `ctxr update`, never hand-edited. The default location is
  * the directory harnesses with skill auto-discovery read, so there is no
  * wrapper and no extra hop; any other harness reaches the same file by
@@ -20,8 +20,8 @@ import { type ScannedDoc } from './conventions.js';
  * that verifies it. The one config-derived skill (placement) is rendered
  * per store, which is why a seed's body is a function of the config.
  */
-export interface Procedure {
-    /** Skill directory slug under config.harness.procedures_path (file is `<slug>/SKILL.md`). */
+export interface Skill {
+    /** Skill directory slug under config.harness.skills_path (file is `<slug>/SKILL.md`). */
     file: string;
     /** The human title (the H1 in the skill body). */
     name: string;
@@ -29,7 +29,7 @@ export interface Procedure {
     description: string;
     content: string;
 }
-interface ProcedureSeed {
+interface SkillSeed {
     file: string;
     name: string;
     description: string;
@@ -39,17 +39,17 @@ interface ProcedureSeed {
 export declare const MANAGED_SKILL_HEADER = "<!-- Owned by contexture \u2014 written by `ctxr init`, refreshed by `ctxr update`. Do not edit; add your own skills alongside. -->";
 export declare function terminatingLayers(config: StoreConfig): TaxonomyLayerConfig[];
 export declare function retiredLayers(config: StoreConfig): TaxonomyLayerConfig[];
-export declare const PROCEDURES: readonly ProcedureSeed[];
+export declare const SKILLS: readonly SkillSeed[];
 /** The owned skills, rendered against one store's configuration — what `syncShippedSkills` writes. */
-export declare function renderProcedures(config: StoreConfig): Procedure[];
+export declare function renderSkills(config: StoreConfig): Skill[];
 /**
  * entry-doc-generation spec: every skill actually on disk — the contexture-
  * owned ones plus any operator-authored ones. This is what the AGENTS.md
- * index and verify --portable consume; the static PROCEDURES const is only
+ * index and verify --portable consume; the static SKILLS const is only
  * the canonical content syncShippedSkills writes.
  */
-export declare function scanProcedures(root: string, config: StoreConfig): Promise<ScannedDoc[]>;
-export declare function procedurePaths(config: StoreConfig): string[];
+export declare function scanSkills(root: string, config: StoreConfig): Promise<ScannedDoc[]>;
+export declare function skillPaths(config: StoreConfig): string[];
 /**
  * Brings every contexture-owned skill copy to the installed package's
  * content: written when missing, rewritten when different (byte-stable —
@@ -61,4 +61,4 @@ export declare function procedurePaths(config: StoreConfig): string[];
  */
 export declare function syncShippedSkills(root: string, config: StoreConfig): Promise<string[]>;
 export {};
-//# sourceMappingURL=procedures.d.ts.map
+//# sourceMappingURL=skills.d.ts.map

package/dist/core/skills.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"skills.d.ts","sourceRoot":"","sources":["../../src/core/skills.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAE,mBAAmB,EAAE,MAAM,qBAAqB,CAAC;AAC5E,OAAO,EAAgC,KAAK,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAcjF;;;;;;;;;;;;;;;;;;;GAmBG;AACH,MAAM,WAAW,KAAK;IACpB,yFAAyF;IACzF,IAAI,EAAE,MAAM,CAAC;IACb,kDAAkD;IAClD,IAAI,EAAE,MAAM,CAAC;IACb,qEAAqE;IACrE,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,UAAU,SAAS;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,+FAA+F;IAC/F,IAAI,EAAE,CAAC,MAAM,EAAE,WAAW,KAAK,MAAM,EAAE,CAAC;CACzC;AAED,eAAO,MAAM,oBAAoB,wIACiG,CAAC;AAYnI,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,WAAW,GAAG,mBAAmB,EAAE,CAE5E;AAED,wBAAgB,aAAa,CAAC,MAAM,EAAE,WAAW,GAAG,mBAAmB,EAAE,CAExE;AA+LD,eAAO,MAAM,MAAM,EAAE,SAAS,SAAS,EAatC,CAAC;AAEF,sGAAsG;AACtG,wBAAgB,YAAY,CAAC,MAAM,EAAE,WAAW,GAAG,KAAK,EAAE,CAOzD;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,UAAU,EAAE,CAAC,CAEnF;AAED,wBAAgB,UAAU,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,EAAE,CAExD;AAED;;;;;;;;GAQG;AACH,wBAAsB,iBAAiB,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CA2C5F"}

package/dist/core/{procedures.js → skills.js}

@@ -1,32 +1,16 @@
-import { readFileSync } from 'node:fs';
 import { mkdir, readdir, readFile, rm } from 'node:fs/promises';
 import path from 'node:path';
-import { fileURLToPath } from 'node:url';
 import { scanDocsDir, SKILL_FILE_NAME } from './conventions.js';
+import { GRAPH_DOCUMENT_RELATIVE_PATH } from './graph/persist.js';
 import { writeFileAtomic } from './fs/atomic.js';
+import { packagedTemplate } from './templates.js';
 /**
- * extract-skill-templates: canonical skill bodies live as plain markdown
- * files under `templates/skills/` (reviewable, diffable, syntax-highlighted)
- * rather than as inline TypeScript string arrays — the same pattern
- * `hooks.ts`'s `templatesDir()` already uses for the git hook templates.
- * Loaded synchronously, once, at module init: `ProcedureSeed.body` is called
- * synchronously from many call sites (including throughout the test suite),
- * and these are fixed, package-bundled files whose content never changes
- * after the process starts — threading `async` through every call site to
- * read a file once would be a large, purely mechanical change for no
- * behavioral gain.
+ * The canonical skill bodies live as plain markdown under
+ * `templates/skills/` — see `templates.ts` for why they are loaded
+ * synchronously and cached.
  */
-function skillTemplatesDir() {
-    return fileURLToPath(new URL('../../templates/skills', import.meta.url));
-}
-const skillTemplateCache = new Map();
 function skillTemplate(slug) {
-    const cached = skillTemplateCache.get(slug);
-    if (cached !== undefined)
-        return cached;
-    const text = readFileSync(path.join(skillTemplatesDir(), `${slug}.md`), 'utf8').replace(/\n$/, '');
-    skillTemplateCache.set(slug, text);
-    return text;
+    return packagedTemplate('skills', slug);
 }
 export const MANAGED_SKILL_HEADER = '<!-- Owned by contexture — written by `ctxr init`, refreshed by `ctxr update`. Do not edit; add your own skills alongside. -->';
 /**
@@ -101,13 +85,13 @@ const INGEST_ORCHESTRATION = {
     file: 'ctxr-ingest-orchestration',
     name: 'Ingest orchestration',
     description: 'Capture raw material into the inbox, run the dedupe check, read the existing cluster, decide new/update/merge/restructure, and ingest with source identity via the contexture CLI.',
-    body: () => skillTemplate('ctxr-ingest-orchestration').split('\n'),
+    body: () => skillTemplate('ctxr-ingest-orchestration').replaceAll('__GRAPH_DOCUMENT_PATH__', GRAPH_DOCUMENT_RELATIVE_PATH).split('\n'),
 };
 const CONNECTION_FINDING = {
     file: 'ctxr-connection-finding',
     name: 'Connection finding',
     description: 'Traverse the wikilink graph of the store (neighbors, paths, hubs, orphans) to find what a note already connects to.',
-    body: () => skillTemplate('ctxr-connection-finding').split('\n'),
+    body: () => skillTemplate('ctxr-connection-finding').replaceAll('__GRAPH_DOCUMENT_PATH__', GRAPH_DOCUMENT_RELATIVE_PATH).split('\n'),
 };
 /**
  * graph-context-document spec: the proposal skill groups by the CONFIGURED
@@ -168,7 +152,7 @@ const LAND = {
 function reclaimingStep(config) {
     if (config.session.workspaces_external) {
         return [
-            'Session worktrees are provided externally (`session.workspaces_external: true`) — this procedure MUST NOT',
+            'Session worktrees are provided externally (`session.workspaces_external: true`) — this skill MUST NOT',
             'create, switch to, unlock, remove, or prune a worktree. `ctxr session reap` refuses to run under this',
             'configuration; reclaiming worktrees is the external process\'s responsibility, not this skill\'s.',
         ];
@@ -205,7 +189,7 @@ const ORGANIZE_AUDIT = {
     description: 'Audit store health with ctxr lint (observations) and ctxr doctor (blocking invariants), retire by moving, and classify broken links before fixing them.',
     body: () => skillTemplate('ctxr-organize-audit').split('\n'),
 };
-export const PROCEDURES = [
+export const SKILLS = [
     INGEST_ORCHESTRATION,
     PLACEMENT,
     CONNECTION_FINDING,
@@ -220,8 +204,8 @@ export const PROCEDURES = [
     ORGANIZE_AUDIT,
 ];
 /** The owned skills, rendered against one store's configuration — what `syncShippedSkills` writes. */
-export function renderProcedures(config) {
-    return PROCEDURES.map((seed) => ({
+export function renderSkills(config) {
+    return SKILLS.map((seed) => ({
         file: seed.file,
         name: seed.name,
         description: seed.description,
@@ -231,14 +215,14 @@ export function renderProcedures(config) {
 /**
  * entry-doc-generation spec: every skill actually on disk — the contexture-
  * owned ones plus any operator-authored ones. This is what the AGENTS.md
- * index and verify --portable consume; the static PROCEDURES const is only
+ * index and verify --portable consume; the static SKILLS const is only
  * the canonical content syncShippedSkills writes.
  */
-export function scanProcedures(root, config) {
-    return scanDocsDir(root, config.harness.procedures_path);
+export function scanSkills(root, config) {
+    return scanDocsDir(root, config.harness.skills_path);
 }
-export function procedurePaths(config) {
-    return PROCEDURES.map((p) => path.join(config.harness.procedures_path, p.file, SKILL_FILE_NAME).split(path.sep).join('/'));
+export function skillPaths(config) {
+    return SKILLS.map((p) => path.join(config.harness.skills_path, p.file, SKILL_FILE_NAME).split(path.sep).join('/'));
 }
 /**
  * Brings every contexture-owned skill copy to the installed package's
@@ -251,9 +235,9 @@ export function procedurePaths(config) {
  */
 export async function syncShippedSkills(root, config) {
     const changed = [];
-    for (const procedure of renderProcedures(config)) {
+    for (const skill of renderSkills(config)) {
         const relativePath = path
-            .join(config.harness.procedures_path, procedure.file, SKILL_FILE_NAME)
+            .join(config.harness.skills_path, skill.file, SKILL_FILE_NAME)
             .split(path.sep)
             .join('/');
         const absolutePath = path.join(root, relativePath);
@@ -264,14 +248,14 @@ export async function syncShippedSkills(root, config) {
         catch {
             existing = undefined;
         }
-        if (existing !== procedure.content) {
+        if (existing !== skill.content) {
             await mkdir(path.dirname(absolutePath), { recursive: true });
-            await writeFileAtomic(absolutePath, procedure.content);
+            await writeFileAtomic(absolutePath, skill.content);
             changed.push(relativePath);
         }
     }
-    const shippedSlugs = new Set(PROCEDURES.map((p) => p.file));
-    const skillsDir = path.join(root, config.harness.procedures_path);
+    const shippedSlugs = new Set(SKILLS.map((p) => p.file));
+    const skillsDir = path.join(root, config.harness.skills_path);
     let entries = [];
     try {
         entries = await readdir(skillsDir, { withFileTypes: true });
@@ -293,8 +277,8 @@ export async function syncShippedSkills(root, config) {
         if (!content.includes(MANAGED_SKILL_HEADER))
             continue; // operator-authored: never touched
         await rm(path.join(skillsDir, entry.name), { recursive: true, force: true });
-        changed.push(path.join(config.harness.procedures_path, entry.name, SKILL_FILE_NAME).split(path.sep).join('/'));
+        changed.push(path.join(config.harness.skills_path, entry.name, SKILL_FILE_NAME).split(path.sep).join('/'));
     }
     return changed;
 }
-//# sourceMappingURL=procedures.js.map
+//# sourceMappingURL=skills.js.map

package/dist/core/skills.js.map

@@ -0,0 +1 @@
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package/dist/core/templates.d.ts

@@ -0,0 +1,20 @@
+/**
+ * `templates/<dir>/<name>.md`, with exactly one trailing newline stripped —
+ * so a template file that looks like a normal file (ends with a newline)
+ * yields the same line array an inline `[...]` literal would have.
+ */
+export declare function packagedTemplate(dir: string, name: string): string;
+/**
+ * Splices a computed list of lines in where `token` sits alone on its own
+ * line. An EMPTY list removes that line entirely, rather than leaving a
+ * blank one behind — which is what a plain `.replace(token, '')` would do,
+ * and is the difference between byte-identical output and a stray blank
+ * line. The empty case is not hypothetical: an index block renders empty
+ * whenever its scanned directory is missing.
+ *
+ * Throws when the token is absent, so a mistyped placeholder name fails at
+ * render time instead of silently shipping the literal `__TOKEN__` string
+ * into a store's AGENTS.md.
+ */
+export declare function substituteBlock(text: string, token: string, lines: readonly string[]): string;
+//# sourceMappingURL=templates.d.ts.map

package/dist/core/templates.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"templates.d.ts","sourceRoot":"","sources":["../../src/core/templates.ts"],"names":[],"mappings":"AA2BA;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,CAOlE;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,CAe7F"}