ctxr-cli 0.3.0 → 0.4.1

package/dist/core/agents-doc.d.ts

@@ -1,16 +1,16 @@
 import type { StoreConfig } from '../config/schema.js';
 import { type ScannedDoc } from './conventions.js';
+export declare function agentsMdPath(root: string): string;
 /**
  * context-retrieval spec (task 4.5): the leg-routing rule that tells an
  * agent which of its two retrieval legs to use for a given question — the
  * catalog/graph (contexture-built-and-maintained) or its own direct content
  * matching (grep, scoped by the store's declared exclusion paths). This is
  * one fenced region within AGENTS.md; Phase 8 adds the canonical template's
- * other sections (root-resolution, frontmatter schema, write-path, procedure
+ * other sections (root-resolution, frontmatter schema, write-path, skill
  * index) as sibling regions in the same file, never touching this one.
  */
 export declare const AGENTS_MD_LEG_ROUTING_FENCE: import("./markers.js").Fence;
-export declare function agentsMdPath(root: string): string;
 export declare function renderLegRoutingSection(config: StoreConfig): string[];
 /** Idempotently reconciles AGENTS.md's leg-routing section from current config — called at init and on re-init. */
 export declare function buildAgentsLegRoutingSection(root: string, config: StoreConfig): Promise<{
@@ -30,12 +30,14 @@ export declare function buildAgentsCaptureSection(root: string, config: StoreCon
     changed: boolean;
 }>;
 /**
- * context-organize spec (task 7.1): the placement procedure is
- * documentation driven entirely by the configured taxonomy, never a
- * hardcoded layout — this section is generated purely from
+ * context-organize spec (task 7.1): the placement skill's documentation is
+ * driven entirely by the configured taxonomy, never a
+ * hardcoded layout — the layer list is generated purely from
  * `config.taxonomy.layers`, so it reads correctly under PARA, Zettelkasten,
  * Diátaxis, or any custom taxonomy without a single layer name appearing in
- * this file's own source.
+ * this file's own source. A store with no declared layers gets its own
+ * template rather than a swapped-out middle, so both variants read as
+ * complete documents.
  */
 export declare const AGENTS_MD_PLACEMENT_FENCE: import("./markers.js").Fence;
 export declare function renderPlacementSection(config: StoreConfig): string[];
@@ -45,12 +47,12 @@ export declare function buildAgentsPlacementSection(root: string, config: StoreC
 /**
  * harness-portability spec (task 8.5): the canonical template's four
  * required pieces — root-resolution rule, frontmatter schema pointer,
- * write-path rule, and a procedure index — so an agent that has read only
+ * write-path rule, and a skill index — so an agent that has read only
  * this file, with no harness-specific context, has everything it needs
  * (the spec's own "Reading only AGENTS.md is sufficient" scenario).
  */
 export declare const AGENTS_MD_CANONICAL_FENCE: import("./markers.js").Fence;
-export declare function renderCanonicalSection(config: StoreConfig, procedures: readonly ScannedDoc[]): string[];
+export declare function renderCanonicalSection(config: StoreConfig, skills: readonly ScannedDoc[]): string[];
 export declare function buildAgentsCanonicalSection(root: string, config: StoreConfig): Promise<{
     changed: boolean;
 }>;
@@ -58,7 +60,9 @@ export declare function buildAgentsCanonicalSection(root: string, config: StoreC
  * entry-doc-generation spec: operator conventions as referenced documents.
  * The index lists what is actually on disk at the configured conventions
  * path; contexture ships no seeds here — conventions are definitionally
- * operator-authored, so an empty store's section explains the mechanism.
+ * operator-authored, so an empty store gets its own template explaining the
+ * mechanism. Both templates end with the same harness-specific-note
+ * paragraph; a test asserts they stay byte-identical.
  */
 export declare const AGENTS_MD_CONVENTIONS_FENCE: import("./markers.js").Fence;
 export declare function renderConventionsSection(config: StoreConfig, conventions: readonly ScannedDoc[]): string[];

package/dist/core/agents-doc.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"agents-doc.d.ts","sourceRoot":"","sources":["../../src/core/agents-doc.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAIvD,OAAO,EAAmB,KAAK,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAsBpE,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAEjD;AAED;;;;;;;;GAQG;AACH,eAAO,MAAM,2BAA2B,8BAA4C,CAAC;AAErF,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,EAAE,CAOrE;AAED,mHAAmH;AACnH,wBAAsB,4BAA4B,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAEnH;AAED;;;;;;;GAOG;AACH,eAAO,MAAM,uBAAuB,8BAAyC,CAAC;AAE9E,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,EAAE,CAElE;AAED,wBAAsB,yBAAyB,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAEhH;AAED;;;;;;;;;GASG;AACH,eAAO,MAAM,yBAAyB,8BAAgC,CAAC;AAEvE,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,EAAE,CAapE;AAED,wBAAsB,2BAA2B,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAElH;AAED;;;;;;GAMG;AACH,eAAO,MAAM,yBAAyB,8BAAgC,CAAC;AAsBvE,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,SAAS,UAAU,EAAE,GAAG,MAAM,EAAE,CAWnG;AAED,wBAAsB,2BAA2B,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAGlH;AAED;;;;;;;GAOG;AACH,eAAO,MAAM,2BAA2B,8BAAwC,CAAC;AAEjF,wBAAgB,wBAAwB,CAAC,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,SAAS,UAAU,EAAE,GAAG,MAAM,EAAE,CAW1G;AAED,wBAAsB,6BAA6B,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAGpH"}

package/dist/core/agents-doc.js

@@ -3,40 +3,40 @@ import { GRAPH_DOCUMENT_RELATIVE_PATH } from './graph/persist.js';
 import { CONFIG_FILE_NAME } from './root.js';
 import { excludedPrefixesFor } from './notes/list.js';
 import { scanConventions } from './conventions.js';
-import { scanProcedures } from './procedures.js';
+import { scanSkills } from './skills.js';
 import { upsertFencedRegionInFile } from './fs/fenced-region.js';
 import { htmlCommentFence } from './markers.js';
+import { packagedTemplate, substituteBlock } from './templates.js';
+/**
+ * extract-agents-doc-templates: each generated AGENTS.md section's prose
+ * lives in `templates/agents/<fence-slug>.md`, named for the fence it lands
+ * in, so the file a reviewer opens and the region it writes share a name.
+ * Only genuinely per-store data — the exclusion list, the taxonomy layers,
+ * the scanned indexes — is computed here and substituted in.
+ */
+function agentsTemplate(name) {
+    return packagedTemplate('agents', name);
+}
+/** The one index-entry format both the skill and convention indexes use. */
+function docIndexEntry(doc) {
+    return `- [${doc.title}](${doc.path})${doc.description ? ` — ${doc.description}` : ''}`;
+}
+export function agentsMdPath(root) {
+    return path.join(root, 'AGENTS.md');
+}
 /**
  * context-retrieval spec (task 4.5): the leg-routing rule that tells an
  * agent which of its two retrieval legs to use for a given question — the
  * catalog/graph (contexture-built-and-maintained) or its own direct content
  * matching (grep, scoped by the store's declared exclusion paths). This is
  * one fenced region within AGENTS.md; Phase 8 adds the canonical template's
- * other sections (root-resolution, frontmatter schema, write-path, procedure
+ * other sections (root-resolution, frontmatter schema, write-path, skill
  * index) as sibling regions in the same file, never touching this one.
  */
 export const AGENTS_MD_LEG_ROUTING_FENCE = htmlCommentFence('retrieval-leg-routing');
-export function agentsMdPath(root) {
-    return path.join(root, 'AGENTS.md');
-}
 export function renderLegRoutingSection(config) {
     const exclusions = [...new Set(excludedPrefixesFor(config))];
-    return [
-        '## Retrieval: which leg to use',
-        '',
-        'contexture builds and maintains two retrieval tools ahead of time — consult them first:',
-        '',
-        '- **Catalog** (`ctxr catalog show --section <id>`): a curated, coverage-guaranteed index of every retrievable note, one section per taxonomy layer.',
-        '- **Graph** (`ctxr graph query ...`): the wikilink graph between notes — neighbors, shortest path, hubs, orphans, clusters, bridges; `--type <relation>` follows one configured relation.',
-        `- **Graph document** (\`${GRAPH_DOCUMENT_RELATIVE_PATH}\`, rebuilt by \`ctxr graph build\`): hub notes by cluster, cross-cluster bridges, and orphans — read it for cluster context before writing.`,
-        '',
-        'For a literal or entity question the catalog and graph do not answer (a specific string, an exact identifier, a phrase),',
-        'use your own direct content-matching tool (e.g. grep/ripgrep) against the store, scoped to exclude:',
-        '',
-        ...exclusions.map((prefix) => `- \`${prefix}\``),
-        '',
-        'There is no `ctxr search` command. Ranked or semantic search is deferred to a future version — do not look for one.',
-    ];
+    return substituteBlock(agentsTemplate('retrieval-leg-routing').replaceAll('__GRAPH_DOCUMENT_PATH__', GRAPH_DOCUMENT_RELATIVE_PATH), '__EXCLUSION_PATHS__', exclusions.map((prefix) => `- \`${prefix}\``)).split('\n');
 }
 /** Idempotently reconciles AGENTS.md's leg-routing section from current config — called at init and on re-init. */
 export async function buildAgentsLegRoutingSection(root, config) {
@@ -52,61 +52,31 @@ export async function buildAgentsLegRoutingSection(root, config) {
  */
 export const AGENTS_MD_CAPTURE_FENCE = htmlCommentFence('capture-and-ingest');
 export function renderCaptureSection(config) {
-    return [
-        '## Capturing and ingesting new material',
-        '',
-        `To capture something new, write a plain markdown file directly into \`${config.ingest.inbox_path}\` —`,
-        'no CLI command wraps this. That file MUST NOT contain any of these frontmatter fields; contexture assigns',
-        'them once, at ingest, and never before:',
-        '',
-        '- `source_type`',
-        '- `source_id`',
-        '- `source_hash`',
-        '- `ingested`',
-        '',
-        'Before ingesting, run `ctxr source check <path> --source-id <id>` to get one of four verdicts:',
-        '`new`, `already_ingested`, `alternate_source_match`, or `multiple_matches` — the last one means stop and',
-        'resolve the ambiguity yourself rather than guessing which existing note it is.',
-        '',
-        'To ingest, run `ctxr ingest <path> --source-type <type> --source-id <id>`. It stamps the four fields',
-        'above onto the file in place and rebuilds the catalog, so the result already has a catalog entry.',
-    ];
+    return agentsTemplate('capture-and-ingest').replaceAll('__INBOX_PATH__', config.ingest.inbox_path).split('\n');
 }
 export async function buildAgentsCaptureSection(root, config) {
     return upsertFencedRegionInFile(agentsMdPath(root), AGENTS_MD_CAPTURE_FENCE, renderCaptureSection(config));
 }
 /**
- * context-organize spec (task 7.1): the placement procedure is
- * documentation driven entirely by the configured taxonomy, never a
- * hardcoded layout — this section is generated purely from
+ * context-organize spec (task 7.1): the placement skill's documentation is
+ * driven entirely by the configured taxonomy, never a
+ * hardcoded layout — the layer list is generated purely from
  * `config.taxonomy.layers`, so it reads correctly under PARA, Zettelkasten,
  * Diátaxis, or any custom taxonomy without a single layer name appearing in
- * this file's own source.
+ * this file's own source. A store with no declared layers gets its own
+ * template rather than a swapped-out middle, so both variants read as
+ * complete documents.
  */
 export const AGENTS_MD_PLACEMENT_FENCE = htmlCommentFence('placement');
 export function renderPlacementSection(config) {
     const { layers } = config.taxonomy;
-    if (layers.length === 0) {
-        return [
-            '## Placing a new note',
-            '',
-            'This store\'s taxonomy declares no top-level layers — place new notes directly at the store root (or',
-            'wherever related notes already live) and rely on wikilinks and `ctxr graph` for organization,',
-            'rather than a folder hierarchy.',
-        ];
-    }
-    const lines = [
-        '## Placing a new note',
-        '',
-        'This store\'s taxonomy declares these layers — choose the one whose description best matches the note:',
-        '',
-    ];
-    for (const layer of layers) {
+    if (layers.length === 0)
+        return agentsTemplate('placement-no-layers').split('\n');
+    const layerLines = layers.map((layer) => {
         const directoryDefault = Object.entries(config.visibility.directory_defaults).find(([prefix]) => prefix === layer.path || prefix === `${layer.path}/`)?.[1];
-        lines.push(`- **${layer.name}** (\`${layer.path}/\`): ${layer.description}${directoryDefault ? ` Notes here default to visibility "${directoryDefault}" unless given an explicit value.` : ''}`);
-    }
-    lines.push('', "If no layer fits, use the store's uncategorized/catch-all location and revisit placement later.");
-    return lines;
+        return `- **${layer.name}** (\`${layer.path}/\`): ${layer.description}${directoryDefault ? ` Notes here default to visibility "${directoryDefault}" unless given an explicit value.` : ''}`;
+    });
+    return substituteBlock(agentsTemplate('placement'), '__LAYER_LIST__', layerLines).split('\n');
 }
 export async function buildAgentsPlacementSection(root, config) {
     return upsertFencedRegionInFile(agentsMdPath(root), AGENTS_MD_PLACEMENT_FENCE, renderPlacementSection(config));
@@ -114,67 +84,59 @@ export async function buildAgentsPlacementSection(root, config) {
 /**
  * harness-portability spec (task 8.5): the canonical template's four
  * required pieces — root-resolution rule, frontmatter schema pointer,
- * write-path rule, and a procedure index — so an agent that has read only
+ * write-path rule, and a skill index — so an agent that has read only
  * this file, with no harness-specific context, has everything it needs
  * (the spec's own "Reading only AGENTS.md is sufficient" scenario).
  */
 export const AGENTS_MD_CANONICAL_FENCE = htmlCommentFence('canonical');
-export function renderCanonicalSection(config, procedures) {
-    const lines = [
-        '## Store fundamentals',
-        '',
-        '### Root resolution',
-        '',
-        `Every contexture command resolves the store root in this order: an explicit ` +
-            '`--root <path>` flag; the `CONTEXTURE_ROOT` environment variable; walking up from the current directory ' +
-            `looking for \`${CONFIG_FILE_NAME}\`. No other flag or environment variable selects the root.`,
-        '',
-        '### Frontmatter schema',
-        '',
-        `- Visibility field: \`${config.fields.visibility}:\` — resolves explicit value, then directory default, then the ` +
-            `configured fail-closed default (\`${config.visibility.default_context}\`). See \`ctxr note resolve <path>\`.`,
-        '- Source-identity fields (assigned only by `ctxr ingest`, never hand-written): `source_type`, `source_id`, `source_hash`, `ingested`.',
-        '- Disclosure audience tags (optional, hand-written): `audience: [<name>, ...]`.',
-        '',
-        '### Write path',
-        '',
-        'Every write to this store happens inside a session worktree, never directly on the default branch: `ctxr ' +
-            'session start` creates one, then `ctxr session submit` validates, commits, pushes, and opens (or ' +
-            'reports how to open) a pull request. Do not edit files in the store root directly.',
-        '',
-        '### Procedure index',
-        '',
-        'Judgment-driven operations, documented as portable markdown under ' +
-            `\`${config.harness.procedures_path}\` — read one directly, no harness-specific discovery required:`,
+/**
+ * context-organize spec: when `organize.mission_path` is configured, the
+ * canonical section names it as a document to load at session start,
+ * immediately after the identity-boundary paragraph. Content is written and
+ * its staleness reported through the existing rollup mechanism (`ctxr
+ * rollup write` / `ctxr rollup stale`) — this pointer only names the path,
+ * it names no mechanism of its own. Nothing is rendered when unset: the
+ * `__MISSION_POINTER__` template line disappears entirely (via
+ * `substituteBlock`'s empty-list case), not a placeholder.
+ */
+function renderMissionPointer(config) {
+    const { mission_path: missionPath } = config.organize;
+    if (!missionPath)
+        return [];
+    return [
         '',
+        `Load \`${missionPath}\` at the start of every session — this store's standing current-state document, ` +
+            'kept current by the mission skill (see the skill index below) and written through `ctxr rollup write`.',
     ];
-    for (const procedure of procedures) {
-        lines.push(`- [${procedure.title}](${procedure.path})${procedure.description ? ` — ${procedure.description}` : ''}`);
-    }
-    return lines;
+}
+export function renderCanonicalSection(config, skills) {
+    const text = substituteBlock(agentsTemplate('canonical')
+        .replaceAll('__CONFIG_FILE_NAME__', CONFIG_FILE_NAME)
+        .replaceAll('__VISIBILITY_FIELD__', config.fields.visibility)
+        .replaceAll('__DEFAULT_CONTEXT__', config.visibility.default_context)
+        .replaceAll('__SKILLS_PATH__', config.harness.skills_path), '__MISSION_POINTER__', renderMissionPointer(config));
+    return substituteBlock(text, '__SKILL_INDEX__', skills.map(docIndexEntry)).split('\n');
 }
 export async function buildAgentsCanonicalSection(root, config) {
-    const procedures = await scanProcedures(root, config);
-    return upsertFencedRegionInFile(agentsMdPath(root), AGENTS_MD_CANONICAL_FENCE, renderCanonicalSection(config, procedures));
+    const skills = await scanSkills(root, config);
+    return upsertFencedRegionInFile(agentsMdPath(root), AGENTS_MD_CANONICAL_FENCE, renderCanonicalSection(config, skills));
 }
 /**
  * entry-doc-generation spec: operator conventions as referenced documents.
  * The index lists what is actually on disk at the configured conventions
  * path; contexture ships no seeds here — conventions are definitionally
- * operator-authored, so an empty store's section explains the mechanism.
+ * operator-authored, so an empty store gets its own template explaining the
+ * mechanism. Both templates end with the same harness-specific-note
+ * paragraph; a test asserts they stay byte-identical.
  */
 export const AGENTS_MD_CONVENTIONS_FENCE = htmlCommentFence('store-conventions');
 export function renderConventionsSection(config, conventions) {
-    const lines = ['## Store conventions', ''];
     if (conventions.length === 0) {
-        lines.push(`This store declares no convention documents yet. Operator-authored conventions (content style, field`, `semantics, house rules) belong as markdown files under \`${config.harness.conventions_path}\` — each is`, 'indexed here on regeneration, referenced by path, never inlined.');
-        return lines;
-    }
-    lines.push('Operator-authored conventions for this store — read the ones relevant to your task:', '');
-    for (const doc of conventions) {
-        lines.push(`- [${doc.title}](${doc.path})${doc.description ? ` — ${doc.description}` : ''}`);
+        return agentsTemplate('store-conventions-empty')
+            .replaceAll('__CONVENTIONS_PATH__', config.harness.conventions_path)
+            .split('\n');
     }
-    return lines;
+    return substituteBlock(agentsTemplate('store-conventions'), '__CONVENTION_INDEX__', conventions.map(docIndexEntry)).split('\n');
 }
 export async function buildAgentsConventionsSection(root, config) {
     const conventions = await scanConventions(root, config);

package/dist/core/agents-doc.js.map

@@ -1 +1 @@
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package/dist/core/checks/integrity-checks.d.ts

@@ -19,6 +19,20 @@ export declare const graphDanglingLinksCheck: import("./types.js").CheckDefiniti
 export declare const schemaVersionCurrencyCheck: import("./types.js").CheckDefinition;
 /** store-integrity spec: "adapter compatibility (per adapters)." */
 export declare const adapterCompatibilityCheck: import("./types.js").CheckDefinition;
+/**
+ * harness-portability spec: "A harness-specific entry file only imports" —
+ * SHALL contain nothing beyond the adapter's own managed import plus that
+ * harness's own extras, and SHALL NOT duplicate canonical content. Exact
+ * prose duplication is undecidable to check in general (paraphrase, partial
+ * copy, reordering), so this catches the concrete failure mode the
+ * requirement is aimed at: a section heading also present in AGENTS.md,
+ * copy-pasted into the entry file outside its managed fence — the way an
+ * operator reaching for "where do I put a Claude-only note" might otherwise
+ * duplicate a whole AGENTS.md section into CLAUDE.md instead of writing a
+ * harness-specific extra beneath the import (see the `store-conventions`
+ * fence's own guidance in `agents-doc.ts`).
+ */
+export declare const harnessEntryNoDuplicateConventionTextCheck: import("./types.js").CheckDefinition;
 /** store-integrity spec: "no unrecognized top-level config keys." */
 export declare const noUnrecognizedConfigKeysCheck: import("./types.js").CheckDefinition;
 export declare const INTEGRITY_CHECKS: import("./types.js").CheckDefinition[];

package/dist/core/checks/integrity-checks.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"integrity-checks.d.ts","sourceRoot":"","sources":["../../../src/core/checks/integrity-checks.ts"],"names":[],"mappings":"AAmBA;;;;;;;GAOG;AACH,eAAO,MAAM,6BAA6B,sCAkCxC,CAAC;AAEH;;;;;;GAMG;AAGH,eAAO,MAAM,uBAAuB,sCAoBlC,CAAC;AAEH,6EAA6E;AAC7E,eAAO,MAAM,0BAA0B,sCAsBrC,CAAC;AAEH,oEAAoE;AACpE,eAAO,MAAM,yBAAyB,sCAuBpC,CAAC;AAEH,qEAAqE;AACrE,eAAO,MAAM,6BAA6B,sCAgBxC,CAAC;AAEH,eAAO,MAAM,gBAAgB,wCAM5B,CAAC"}
+{"version":3,"file":"integrity-checks.d.ts","sourceRoot":"","sources":["../../../src/core/checks/integrity-checks.ts"],"names":[],"mappings":"AAwBA;;;;;;;GAOG;AACH,eAAO,MAAM,6BAA6B,sCAkCxC,CAAC;AAEH;;;;;;GAMG;AAGH,eAAO,MAAM,uBAAuB,sCAoBlC,CAAC;AAEH,6EAA6E;AAC7E,eAAO,MAAM,0BAA0B,sCAsBrC,CAAC;AAEH,oEAAoE;AACpE,eAAO,MAAM,yBAAyB,sCAuBpC,CAAC;AAYH;;;;;;;;;;;;GAYG;AACH,eAAO,MAAM,0CAA0C,sCAgDrD,CAAC;AAEH,qEAAqE;AACrE,eAAO,MAAM,6BAA6B,sCAgBxC,CAAC;AAEH,eAAO,MAAM,gBAAgB,wCAO5B,CAAC"}

package/dist/core/checks/integrity-checks.js

@@ -1,7 +1,12 @@
-import { resolveAdapter } from '../../adapters/registry.js';
+import { readFile } from 'node:fs/promises';
+import path from 'node:path';
+import { configuredAdapters, resolveAdapter } from '../../adapters/registry.js';
 import { StoreConfigSchema, SUPPORTED_SCHEMA_VERSION } from '../../config/schema.js';
+import { agentsMdPath } from '../agents-doc.js';
 import { checkCatalogStale } from '../catalog/build.js';
+import { removeFencedRegion } from '../fs/fenced-region.js';
 import { buildGraphFromNotes, graphBuildOptions } from '../graph/model.js';
+import { harnessEntryFence } from '../markers.js';
 import { defineCheck } from './types.js';
 /**
  * store-integrity spec: "unrecognized top-level config keys." StoreConfigSchema
@@ -134,6 +139,76 @@ export const adapterCompatibilityCheck = defineCheck({
         return { status: findings.length > 0 ? 'fail' : 'pass', findings };
     },
 });
+const MARKDOWN_HEADING_RE = /^#{1,6}\s+(.+)$/gm;
+function headingsOf(text) {
+    const headings = new Set();
+    for (const match of text.matchAll(MARKDOWN_HEADING_RE)) {
+        headings.add(match[1].trim().toLowerCase());
+    }
+    return headings;
+}
+/**
+ * harness-portability spec: "A harness-specific entry file only imports" —
+ * SHALL contain nothing beyond the adapter's own managed import plus that
+ * harness's own extras, and SHALL NOT duplicate canonical content. Exact
+ * prose duplication is undecidable to check in general (paraphrase, partial
+ * copy, reordering), so this catches the concrete failure mode the
+ * requirement is aimed at: a section heading also present in AGENTS.md,
+ * copy-pasted into the entry file outside its managed fence — the way an
+ * operator reaching for "where do I put a Claude-only note" might otherwise
+ * duplicate a whole AGENTS.md section into CLAUDE.md instead of writing a
+ * harness-specific extra beneath the import (see the `store-conventions`
+ * fence's own guidance in `agents-doc.ts`).
+ */
+export const harnessEntryNoDuplicateConventionTextCheck = defineCheck({
+    id: 'adapters.harness_entry_no_duplicate_convention_text',
+    title: 'A harness entry file carries no convention text already indexed in AGENTS.md',
+    severity: 'invariant',
+    capability: 'harness-portability',
+    scopes: ['store'],
+    async run(ctx) {
+        const adapters = configuredAdapters(ctx.config, 'harness-generation');
+        if (adapters.length === 0) {
+            return { status: 'pass', findings: [] };
+        }
+        let agentsMdContent;
+        try {
+            agentsMdContent = await readFile(agentsMdPath(ctx.storeRoot), 'utf8');
+        }
+        catch (err) {
+            if (err.code === 'ENOENT') {
+                return { status: 'skip', skipReason: 'AGENTS.md has not been generated yet — run `ctxr update`', findings: [] };
+            }
+            throw err;
+        }
+        const agentsMdHeadings = headingsOf(agentsMdContent);
+        const findings = [];
+        for (const adapter of adapters) {
+            let entryContent;
+            try {
+                entryContent = await readFile(path.join(ctx.storeRoot, adapter.entryFileName), 'utf8');
+            }
+            catch (err) {
+                if (err.code === 'ENOENT')
+                    continue; // nothing generated for this adapter yet
+                throw err;
+            }
+            const extra = removeFencedRegion(entryContent, harnessEntryFence(adapter.id)).text;
+            for (const heading of headingsOf(extra)) {
+                if (agentsMdHeadings.has(heading)) {
+                    findings.push({
+                        code: 'adapters.harness_entry_duplicates_agents_md',
+                        severity: 'error',
+                        message: `"${adapter.entryFileName}" duplicates AGENTS.md's "${heading}" section outside its managed import — canonical content belongs only in AGENTS.md; a harness-specific extra belongs below the import instead.`,
+                        subject: adapter.entryFileName,
+                        details: { heading },
+                    });
+                }
+            }
+        }
+        return { status: findings.length > 0 ? 'fail' : 'pass', findings };
+    },
+});
 /** store-integrity spec: "no unrecognized top-level config keys." */
 export const noUnrecognizedConfigKeysCheck = defineCheck({
     id: 'store.no_unrecognized_config_keys',
@@ -157,6 +232,7 @@ export const INTEGRITY_CHECKS = [
     graphDanglingLinksCheck,
     schemaVersionCurrencyCheck,
     adapterCompatibilityCheck,
+    harnessEntryNoDuplicateConventionTextCheck,
     noUnrecognizedConfigKeysCheck,
 ];
 //# sourceMappingURL=integrity-checks.js.map

package/dist/core/checks/integrity-checks.js.map

@@ -1 +1 @@
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package/dist/core/conventions.d.ts

@@ -1,7 +1,7 @@
 import type { StoreConfig } from '../config/schema.js';
 /**
  * harness-portability spec (entry-doc-generation): operator-authored
- * convention documents and (via scanProcedures in procedures.ts) procedure
+ * convention documents and (via scanSkills in skills.ts) skill
  * files are indexed from what is actually on disk — adding a file is the
  * entire integration. Metadata extraction order: frontmatter title →
  * first `# ` heading → filename stem; description only from frontmatter.

package/dist/core/errors.d.ts

@@ -42,6 +42,15 @@ export declare class SessionNotFoundError extends ContextureError {
 export declare class SessionValidationFailedError extends ContextureError {
     constructor(findings: Finding[]);
 }
+/**
+ * write-lifecycle spec: `session.workspaces_external: true` marks a store
+ * whose worktrees are created/removed by a process outside `ctxr` — `ctxr
+ * session reap` refuses before inspecting or modifying any worktree, rather
+ * than reclaiming something it does not own.
+ */
+export declare class SessionReapWorkspacesExternalError extends ContextureError {
+    constructor();
+}
 export declare class NoRemoteConfiguredError extends ContextureError {
     constructor();
 }

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

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package/dist/core/errors.js

@@ -99,6 +99,22 @@ export class SessionValidationFailedError extends ContextureError {
         });
     }
 }
+/**
+ * write-lifecycle spec: `session.workspaces_external: true` marks a store
+ * whose worktrees are created/removed by a process outside `ctxr` — `ctxr
+ * session reap` refuses before inspecting or modifying any worktree, rather
+ * than reclaiming something it does not own.
+ */
+export class SessionReapWorkspacesExternalError extends ContextureError {
+    constructor() {
+        super(ExitCode.Usage, {
+            code: 'session.reap.workspaces_external',
+            severity: 'error',
+            message: '"session.workspaces_external" is true; "ctxr session reap" refuses to run — worktrees are provided ' +
+                'externally and are not this command\'s to reclaim.',
+        });
+    }
+}
 export class NoRemoteConfiguredError extends ContextureError {
     constructor() {
         super(ExitCode.Usage, {
@@ -123,7 +139,8 @@ export class SessionLandOnDefaultBranchError extends ContextureError {
         super(ExitCode.Usage, {
             code: 'session.land.default_branch',
             severity: 'error',
-            message: `"${branch}" is the store's default branch; "ctxr session land" refuses to land it.`,
+            message: `"${branch}" is the store's default branch; "ctxr session land" refuses to land it. ` +
+                'Name the session with --branch <name>, or the pull request with --pr <number>.',
             subject: branch,
         });
     }