ctxr-cli 0.4.1 → 0.6.0

package/dist/core/browse/routes.js

@@ -0,0 +1,56 @@
+import { readdir } from 'node:fs/promises';
+import path from 'node:path';
+import { catalogSectionsFor, sectionFileName } from '../catalog/model.js';
+import { graphDocumentPath } from '../graph/persist.js';
+import { listNotes } from '../notes/list.js';
+async function walkFiles(root, relative = '') {
+    let entries;
+    try {
+        entries = await readdir(path.join(root, relative), { withFileTypes: true });
+    }
+    catch (err) {
+        if (err.code === 'ENOENT')
+            return [];
+        throw err;
+    }
+    const files = [];
+    for (const entry of entries) {
+        const entryRelative = relative ? `${relative}/${entry.name}` : entry.name;
+        if (entry.isDirectory()) {
+            files.push(...(await walkFiles(root, entryRelative)));
+        }
+        else if (entry.isFile()) {
+            files.push({ urlPath: entryRelative, absolutePath: path.join(root, entryRelative) });
+        }
+    }
+    return files;
+}
+/**
+ * local-browsing-surface design.md D2: built fresh from the store's own
+ * enumeration on every call, never cached — so a path outside every
+ * configured location is absent from the table by construction, and a
+ * request for it is an ordinary lookup miss rather than a check that could
+ * be forgotten on one route and not another.
+ */
+export async function buildRouteTable(store) {
+    const noteList = await listNotes(store.root, store.config);
+    const notes = new Map(noteList.map((note) => [note.path, note]));
+    const catalog = new Map(catalogSectionsFor(store.config).map((section) => [
+        section.id,
+        { id: section.id, absolutePath: path.join(store.root, store.config.catalog.path, sectionFileName(section)) },
+    ]));
+    const publishRoot = path.join(store.root, store.config.publish.path);
+    const publishFiles = new Map((await walkFiles(publishRoot)).map((file) => [file.urlPath, file]));
+    return { notes, catalog, graphDocumentPath: graphDocumentPath(store), publishFiles };
+}
+/** The distinct top-level page folders under the publish route, for the index page. */
+export function publishSlugs(table) {
+    const slugs = new Set();
+    for (const urlPath of table.publishFiles.keys()) {
+        const slug = urlPath.split('/')[0];
+        if (slug)
+            slugs.add(slug);
+    }
+    return [...slugs].sort();
+}
+//# sourceMappingURL=routes.js.map

package/dist/core/browse/routes.js.map

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

@@ -0,0 +1,4 @@
+/** Wraps rendered body HTML in the shared page shell, substituting both slots exactly once each. */
+export declare function renderShell(title: string, bodyHtml: string): Promise<string>;
+export declare function readStylesheet(): Promise<string>;
+//# sourceMappingURL=templates.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"templates.d.ts","sourceRoot":"","sources":["../../../src/core/browse/templates.ts"],"names":[],"mappings":"AAoBA,oGAAoG;AACpG,wBAAsB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAGlF;AAED,wBAAsB,cAAc,IAAI,OAAO,CAAC,MAAM,CAAC,CAEtD"}

package/dist/core/browse/templates.js

@@ -0,0 +1,26 @@
+import { readFile } from 'node:fs/promises';
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+/**
+ * local-browsing-surface design.md D7: shell.html/style.css are markup and
+ * CSS, not markdown fragments meant for splicing, so they don't fit
+ * `packagedTemplate()`'s contract (strips exactly one trailing newline from
+ * a `.md` file, for `substituteBlock`'s line-array callers). This mirrors
+ * `hooks.ts`'s own small async reader for the same reason: a different file
+ * type needs a different loading contract, not a stretched shared one.
+ */
+function templatesDir() {
+    return fileURLToPath(new URL('../../../templates/serve', import.meta.url));
+}
+async function readServeTemplate(fileName) {
+    return readFile(path.join(templatesDir(), fileName), 'utf8');
+}
+/** Wraps rendered body HTML in the shared page shell, substituting both slots exactly once each. */
+export async function renderShell(title, bodyHtml) {
+    const shell = await readServeTemplate('shell.html');
+    return shell.replace('{{TITLE}}', title).replace('{{BODY}}', bodyHtml);
+}
+export async function readStylesheet() {
+    return readServeTemplate('style.css');
+}
+//# sourceMappingURL=templates.js.map

package/dist/core/browse/templates.js.map

@@ -0,0 +1 @@
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package/dist/core/checks/harness-portability-checks.d.ts

@@ -0,0 +1,12 @@
+/**
+ * compose-store-guidance-documents design.md D6: inlining every convention
+ * file's full body into AGENTS.md's "Store conventions" section
+ * (inline-conventions-and-mission) removed the natural size bound an index
+ * provided — an unbounded custom part could make AGENTS.md unwieldy. A
+ * configured ceiling (`harness.convention_max_bytes`, defaulting to
+ * `DEFAULT_CONVENTION_MAX_BYTES`) fails doctor loud rather than silently
+ * truncating content the inlining exists to surface.
+ */
+export declare const conventionsSectionSizeCheck: import("./types.js").CheckDefinition;
+export declare const HARNESS_PORTABILITY_CHECKS: import("./types.js").CheckDefinition[];
+//# sourceMappingURL=harness-portability-checks.d.ts.map

package/dist/core/checks/harness-portability-checks.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"harness-portability-checks.d.ts","sourceRoot":"","sources":["../../../src/core/checks/harness-portability-checks.ts"],"names":[],"mappings":"AAMA;;;;;;;;GAQG;AACH,eAAO,MAAM,2BAA2B,sCAuBtC,CAAC;AAEH,eAAO,MAAM,0BAA0B,wCAAgC,CAAC"}

package/dist/core/checks/harness-portability-checks.js

@@ -0,0 +1,39 @@
+import { DEFAULT_CONVENTION_MAX_BYTES } from '../../config/defaults.js';
+import { AGENTS_MD_CONVENTIONS_FENCE, agentsMdPath } from '../agents-doc.js';
+import { readFencedRegionFromFile } from '../fs/fenced-region.js';
+import { defineCheck } from './types.js';
+/**
+ * compose-store-guidance-documents design.md D6: inlining every convention
+ * file's full body into AGENTS.md's "Store conventions" section
+ * (inline-conventions-and-mission) removed the natural size bound an index
+ * provided — an unbounded custom part could make AGENTS.md unwieldy. A
+ * configured ceiling (`harness.convention_max_bytes`, defaulting to
+ * `DEFAULT_CONVENTION_MAX_BYTES`) fails doctor loud rather than silently
+ * truncating content the inlining exists to surface.
+ */
+export const conventionsSectionSizeCheck = defineCheck({
+    id: 'harness_portability.conventions_section_size',
+    title: "AGENTS.md's inlined \"Store conventions\" section stays within its configured size budget",
+    severity: 'invariant',
+    capability: 'harness-portability',
+    scopes: ['store'],
+    async run(ctx) {
+        const region = await readFencedRegionFromFile(agentsMdPath(ctx.storeRoot), AGENTS_MD_CONVENTIONS_FENCE);
+        if (region.length === 0) {
+            return { status: 'skip', skipReason: 'AGENTS.md has not been generated yet — run `ctxr update`', findings: [] };
+        }
+        const size = Buffer.byteLength(region.join('\n'), 'utf8');
+        const budget = ctx.config.harness.convention_max_bytes ?? DEFAULT_CONVENTION_MAX_BYTES;
+        if (size <= budget)
+            return { status: 'pass', findings: [] };
+        const finding = {
+            code: 'harness_portability.conventions_section_size_exceeded',
+            severity: 'error',
+            message: `AGENTS.md's "Store conventions" section is ${size} bytes, exceeding the configured budget of ${budget}. Trim a convention file's content or raise \`harness.convention_max_bytes\`.`,
+            details: { size, budget },
+        };
+        return { status: 'fail', findings: [finding] };
+    },
+});
+export const HARNESS_PORTABILITY_CHECKS = [conventionsSectionSizeCheck];
+//# sourceMappingURL=harness-portability-checks.js.map

package/dist/core/checks/harness-portability-checks.js.map

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

@@ -8,17 +8,33 @@
  */
 export declare const derivedArtifactStalenessCheck: import("./types.js").CheckDefinition;
 /**
- * store-integrity spec: "dangling links... (per context-retrieval)." A
+ * store-integrity spec: "ambiguous link resolution... (per context-retrieval)." A
  * genuine identity collision is NOT re-checked here — buildGraphFromNotes
  * refuses to persist a graph that has one (core/graph/model.ts), so a
  * persisted graph.json is proof by construction that none exists; there is
  * nothing for a doctor check to find after the fact.
+ *
+ * `graph.dangling` covers two reasons (core/graph/model.ts: DanglingReason).
+ * They're split by owner, not shared: a link that resolves to no note at all
+ * (`not_found`) can't be told apart from a healthy forward reference, so it's
+ * lint's alone (organize-checks.ts:brokenLinksCheck, observation, code
+ * organize.broken_link). A link that resolves ambiguously, to more than one
+ * note (`ambiguous`), is always a mechanical defect with a fix (alias
+ * syntax) — never a legitimate "leave it" case — so it's this check's alone.
  */
-export declare const graphDanglingLinksCheck: import("./types.js").CheckDefinition;
+export declare const graphAmbiguousLinksCheck: import("./types.js").CheckDefinition;
 /** store-integrity spec: "schema version currency (per store-lifecycle)." */
 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 (vendored-craft-skills): "a broken bridge is
+ * detected and repaired" — the read-only half. A harness whose effective
+ * directory already equals the configured skills path has no bridge to
+ * check (same as `bridgeHarnessSkills` skipping it, per the adapters spec's
+ * "no bridge is created" scenario).
+ */
+export declare const harnessSkillsBridgeCheck: 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
@@ -29,11 +45,35 @@ export declare const adapterCompatibilityCheck: import("./types.js").CheckDefini
  * 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`
+ * harness-specific extra beneath the import (see the `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;
+/**
+ * harness-portability spec (inline-conventions-and-mission): "The entry
+ * document's inlined content matches its sources" — `AGENTS.md`'s inlined
+ * conventions/mission sections are derived content (rendered from
+ * `.contexture/conventions/*.md` and the configured mission path), so
+ * editing a source directly without regenerating `AGENTS.md` (e.g. bypassing
+ * `ctxr update`) leaves it silently stale. Reuses `checkAgentsMdDrift`, the
+ * same re-render-and-diff `ctxr verify --portable` uses, so the two commands
+ * can never disagree about whether a store is in sync.
+ */
+export declare const agentsMdInlinedContentCurrentCheck: import("./types.js").CheckDefinition;
+/**
+ * write-lifecycle spec / harness-portability spec (inline-conventions-and-mission):
+ * "A commit that would leave the entry document stale is refused." The
+ * store-scope drift check above reads the working tree, which is the wrong
+ * source of truth for a pre-commit hook — an operator can edit a convention
+ * file, forget to run `ctxr update`, and `git add` only the convention file;
+ * the working tree would then have a regenerated AGENTS.md sitting right
+ * next to it only if they happened to run `ctxr update` first, which is
+ * exactly the step this check exists to enforce. So this reads STAGED
+ * content for any file this commit touches (falling back to disk for files
+ * the commit doesn't touch) and re-renders against that view instead.
+ */
+export declare const stagedAgentsMdInlinedContentCurrentCheck: import("./types.js").CheckDefinition;
 export declare const INTEGRITY_CHECKS: import("./types.js").CheckDefinition[];
 //# sourceMappingURL=integrity-checks.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"integrity-checks.d.ts","sourceRoot":"","sources":["../../../src/core/checks/integrity-checks.ts"],"names":[],"mappings":"AAkCA;;;;;;;GAOG;AACH,eAAO,MAAM,6BAA6B,sCAkCxC,CAAC;AAEH;;;;;;;;;;;;;;GAcG;AACH,eAAO,MAAM,wBAAwB,sCAsBnC,CAAC;AAEH,6EAA6E;AAC7E,eAAO,MAAM,0BAA0B,sCAsBrC,CAAC;AAEH,oEAAoE;AACpE,eAAO,MAAM,yBAAyB,sCAuBpC,CAAC;AAEH;;;;;;GAMG;AACH,eAAO,MAAM,wBAAwB,sCAwBnC,CAAC;AAYH;;;;;;;;;;;;GAYG;AACH,eAAO,MAAM,0CAA0C,sCAiDrD,CAAC;AAEH,qEAAqE;AACrE,eAAO,MAAM,6BAA6B,sCAgBxC,CAAC;AAEH;;;;;;;;;GASG;AACH,eAAO,MAAM,kCAAkC,sCA4B7C,CAAC;AAqBH;;;;;;;;;;;GAWG;AACH,eAAO,MAAM,wCAAwC,sCAiEnD,CAAC;AAEH,eAAO,MAAM,gBAAgB,wCAU5B,CAAC"}

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

@@ -2,10 +2,12 @@ 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 { AGENTS_MD_CONVENTIONS_FENCE, AGENTS_MD_MISSION_FENCE, agentsMdPath, checkAgentsMdDrift, renderConventionsSection, renderMissionSection, } from '../agents-doc.js';
 import { checkCatalogStale } from '../catalog/build.js';
-import { removeFencedRegion } from '../fs/fenced-region.js';
+import { extractDocMetadata, scanConventions } from '../conventions.js';
+import { readFencedRegion, removeFencedRegion } from '../fs/fenced-region.js';
 import { buildGraphFromNotes, graphBuildOptions } from '../graph/model.js';
+import { effectiveSkillsDir, isBridgeBroken } from '../harness/bridge.js';
 import { harnessEntryFence } from '../markers.js';
 import { defineCheck } from './types.js';
 /**
@@ -60,17 +62,23 @@ export const derivedArtifactStalenessCheck = defineCheck({
     },
 });
 /**
- * store-integrity spec: "dangling links... (per context-retrieval)." A
+ * store-integrity spec: "ambiguous link resolution... (per context-retrieval)." A
  * genuine identity collision is NOT re-checked here — buildGraphFromNotes
  * refuses to persist a graph that has one (core/graph/model.ts), so a
  * persisted graph.json is proof by construction that none exists; there is
  * nothing for a doctor check to find after the fact.
+ *
+ * `graph.dangling` covers two reasons (core/graph/model.ts: DanglingReason).
+ * They're split by owner, not shared: a link that resolves to no note at all
+ * (`not_found`) can't be told apart from a healthy forward reference, so it's
+ * lint's alone (organize-checks.ts:brokenLinksCheck, observation, code
+ * organize.broken_link). A link that resolves ambiguously, to more than one
+ * note (`ambiguous`), is always a mechanical defect with a fix (alias
+ * syntax) — never a legitimate "leave it" case — so it's this check's alone.
  */
-// Shares detection with organize-checks.ts:brokenLinksCheck (lint, observation) under a
-// different id (task 9.4: two ids, two severity lanes, one condition, never double-counted).
-export const graphDanglingLinksCheck = defineCheck({
-    id: 'graph.dangling_links',
-    title: 'The graph has no dangling links',
+export const graphAmbiguousLinksCheck = defineCheck({
+    id: 'graph.ambiguous_links',
+    title: 'The graph has no ambiguous links',
     severity: 'invariant',
     capability: 'context-retrieval',
     scopes: ['store'],
@@ -79,10 +87,12 @@ export const graphDanglingLinksCheck = defineCheck({
         if (!graph) {
             return { status: 'skip', skipReason: 'graph has not been built yet — run `ctxr graph build`', findings: [] };
         }
-        const findings = graph.dangling.map((d) => ({
-            code: 'graph.dangling_link',
+        const findings = graph.dangling
+            .filter((d) => d.reason === 'ambiguous')
+            .map((d) => ({
+            code: 'graph.ambiguous_link',
             severity: 'error',
-            message: `"${d.from}" links to "${d.target}", which is ${d.reason === 'ambiguous' ? 'ambiguous' : 'not found'}.`,
+            message: `"${d.from}" links to "${d.target}", which is ambiguous.`,
             subject: d.from,
             details: { target: d.target, reason: d.reason },
         }));
@@ -139,6 +149,39 @@ export const adapterCompatibilityCheck = defineCheck({
         return { status: findings.length > 0 ? 'fail' : 'pass', findings };
     },
 });
+/**
+ * harness-portability spec (vendored-craft-skills): "a broken bridge is
+ * detected and repaired" — the read-only half. A harness whose effective
+ * directory already equals the configured skills path has no bridge to
+ * check (same as `bridgeHarnessSkills` skipping it, per the adapters spec's
+ * "no bridge is created" scenario).
+ */
+export const harnessSkillsBridgeCheck = defineCheck({
+    id: 'harness_portability.skills_bridge',
+    title: 'Every declared harness\'s skills directory resolves to the canonical skills path',
+    severity: 'invariant',
+    capability: 'harness-portability',
+    scopes: ['store'],
+    async run(ctx) {
+        const canonical = ctx.config.harness.skills_path;
+        const findings = [];
+        for (const adapter of configuredAdapters(ctx.config, 'harness-generation')) {
+            const harnessDir = effectiveSkillsDir(ctx.config, adapter.id, adapter.skillsDir);
+            if (harnessDir === canonical)
+                continue;
+            if (await isBridgeBroken(ctx.storeRoot, canonical, harnessDir)) {
+                findings.push({
+                    code: 'harness_portability.broken_bridge',
+                    severity: 'error',
+                    message: `"${harnessDir}" (${adapter.id}) does not resolve to the configured skills path "${canonical}" — run \`ctxr update\` to repair it.`,
+                    subject: adapter.id,
+                    details: { path: harnessDir, canonical },
+                });
+            }
+        }
+        return { status: findings.length > 0 ? 'fail' : 'pass', findings };
+    },
+});
 const MARKDOWN_HEADING_RE = /^#{1,6}\s+(.+)$/gm;
 function headingsOf(text) {
     const headings = new Set();
@@ -157,7 +200,7 @@ function headingsOf(text) {
  * 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`
+ * harness-specific extra beneath the import (see the `conventions`
  * fence's own guidance in `agents-doc.ts`).
  */
 export const harnessEntryNoDuplicateConventionTextCheck = defineCheck({
@@ -184,6 +227,8 @@ export const harnessEntryNoDuplicateConventionTextCheck = defineCheck({
         const agentsMdHeadings = headingsOf(agentsMdContent);
         const findings = [];
         for (const adapter of adapters) {
+            if (adapter.entryFileName === undefined)
+                continue; // skills-only adapter — no entry file to check
             let entryContent;
             try {
                 entryContent = await readFile(path.join(ctx.storeRoot, adapter.entryFileName), 'utf8');
@@ -227,12 +272,145 @@ export const noUnrecognizedConfigKeysCheck = defineCheck({
         return { status: findings.length > 0 ? 'fail' : 'pass', findings };
     },
 });
+/**
+ * harness-portability spec (inline-conventions-and-mission): "The entry
+ * document's inlined content matches its sources" — `AGENTS.md`'s inlined
+ * conventions/mission sections are derived content (rendered from
+ * `.contexture/conventions/*.md` and the configured mission path), so
+ * editing a source directly without regenerating `AGENTS.md` (e.g. bypassing
+ * `ctxr update`) leaves it silently stale. Reuses `checkAgentsMdDrift`, the
+ * same re-render-and-diff `ctxr verify --portable` uses, so the two commands
+ * can never disagree about whether a store is in sync.
+ */
+export const agentsMdInlinedContentCurrentCheck = defineCheck({
+    id: 'harness_portability.agents_md_inlined_content_current',
+    title: "AGENTS.md's inlined conventions and mission content match their source files",
+    severity: 'invariant',
+    capability: 'harness-portability',
+    scopes: ['store'],
+    async run(ctx) {
+        const drift = await checkAgentsMdDrift(ctx.storeRoot, ctx.config);
+        const findings = [
+            ...drift.driftedConventions.map((conventionPath) => ({
+                code: 'harness_portability.agents_md_convention_drifted',
+                severity: 'error',
+                message: `AGENTS.md's "Store conventions" section no longer matches "${conventionPath}" — run \`ctxr update\`.`,
+                subject: conventionPath,
+            })),
+            ...(drift.driftedMission
+                ? [
+                    {
+                        code: 'harness_portability.agents_md_mission_drifted',
+                        severity: 'error',
+                        message: `AGENTS.md's "Mission" section no longer matches "${drift.driftedMission}" — run \`ctxr update\`.`,
+                        subject: drift.driftedMission,
+                    },
+                ]
+                : []),
+        ];
+        return { status: findings.length > 0 ? 'fail' : 'pass', findings };
+    },
+});
+/**
+ * A path's staged (index) content when it's part of this commit, else its
+ * current on-disk content — the pre-commit-hook analogue of
+ * `checkAgentsMdDrift`'s working-tree reads, so a staged-but-not-yet-merged
+ * edit to a source file is seen even though nothing has been committed yet.
+ * `null` means the path doesn't exist in either the staged set or on disk
+ * (deleted, or staged as a deletion).
+ */
+async function stagedOrDiskContent(storeRoot, staged, relativePath) {
+    const stagedFile = staged.find((f) => f.path === relativePath);
+    if (stagedFile)
+        return stagedFile.status === 'D' ? null : (stagedFile.content ?? null);
+    try {
+        return await readFile(path.join(storeRoot, relativePath), 'utf8');
+    }
+    catch (err) {
+        if (err.code === 'ENOENT')
+            return null;
+        throw err;
+    }
+}
+/**
+ * write-lifecycle spec / harness-portability spec (inline-conventions-and-mission):
+ * "A commit that would leave the entry document stale is refused." The
+ * store-scope drift check above reads the working tree, which is the wrong
+ * source of truth for a pre-commit hook — an operator can edit a convention
+ * file, forget to run `ctxr update`, and `git add` only the convention file;
+ * the working tree would then have a regenerated AGENTS.md sitting right
+ * next to it only if they happened to run `ctxr update` first, which is
+ * exactly the step this check exists to enforce. So this reads STAGED
+ * content for any file this commit touches (falling back to disk for files
+ * the commit doesn't touch) and re-renders against that view instead.
+ */
+export const stagedAgentsMdInlinedContentCurrentCheck = defineCheck({
+    id: 'staged.agents_md_inlined_content_current',
+    title: 'A staged convention or mission change also stages a matching AGENTS.md regeneration',
+    severity: 'invariant',
+    capability: 'harness-portability',
+    scopes: ['staged'],
+    async run(ctx) {
+        const staged = ctx.staged ?? [];
+        const conventionsPrefix = ctx.config.harness.guidance_path.endsWith('/')
+            ? ctx.config.harness.guidance_path
+            : `${ctx.config.harness.guidance_path}/`;
+        const missionPath = ctx.config.organize.mission_path;
+        const relevantSourceStaged = staged.some((f) => f.path.startsWith(conventionsPrefix) || f.path === missionPath);
+        if (!relevantSourceStaged)
+            return { status: 'pass', findings: [] };
+        const agentsMdStaged = staged.find((f) => f.path === 'AGENTS.md');
+        if (!agentsMdStaged || agentsMdStaged.content === undefined) {
+            return {
+                status: 'fail',
+                findings: [
+                    {
+                        code: 'staged.agents_md_inlined_content_current.not_staged',
+                        severity: 'error',
+                        message: 'This commit stages a change to an operator convention file or the mission document, but not AGENTS.md — run `ctxr update` and stage the result.',
+                    },
+                ],
+            };
+        }
+        const conventions = await scanConventions(ctx.storeRoot, ctx.config);
+        const effectiveConventions = await Promise.all(conventions.map(async (doc) => {
+            const raw = await stagedOrDiskContent(ctx.storeRoot, staged, doc.path);
+            return raw === null ? doc : extractDocMetadata(raw, doc.path);
+        }));
+        const freshConventions = renderConventionsSection(ctx.config, effectiveConventions).join('\n');
+        const stagedConventionsRegion = readFencedRegion(agentsMdStaged.content, AGENTS_MD_CONVENTIONS_FENCE).join('\n');
+        const findings = [];
+        if (freshConventions !== stagedConventionsRegion) {
+            findings.push({
+                code: 'staged.agents_md_inlined_content_current.conventions_mismatch',
+                severity: 'error',
+                message: 'The staged AGENTS.md does not reflect the staged convention file content — run `ctxr update` and re-stage AGENTS.md.',
+            });
+        }
+        if (missionPath) {
+            const missionRaw = await stagedOrDiskContent(ctx.storeRoot, staged, missionPath);
+            const freshMission = renderMissionSection(ctx.config, missionRaw).join('\n');
+            const stagedMissionRegion = readFencedRegion(agentsMdStaged.content, AGENTS_MD_MISSION_FENCE).join('\n');
+            if (freshMission !== stagedMissionRegion) {
+                findings.push({
+                    code: 'staged.agents_md_inlined_content_current.mission_mismatch',
+                    severity: 'error',
+                    message: 'The staged AGENTS.md does not reflect the staged mission document content — run `ctxr update` and re-stage AGENTS.md.',
+                });
+            }
+        }
+        return { status: findings.length > 0 ? 'fail' : 'pass', findings };
+    },
+});
 export const INTEGRITY_CHECKS = [
     derivedArtifactStalenessCheck,
-    graphDanglingLinksCheck,
+    graphAmbiguousLinksCheck,
     schemaVersionCurrencyCheck,
     adapterCompatibilityCheck,
     harnessEntryNoDuplicateConventionTextCheck,
+    harnessSkillsBridgeCheck,
     noUnrecognizedConfigKeysCheck,
+    agentsMdInlinedContentCurrentCheck,
+    stagedAgentsMdInlinedContentCurrentCheck,
 ];
 //# sourceMappingURL=integrity-checks.js.map

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package/dist/core/checks/manifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../../src/core/checks/manifest.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAElD;;;GAGG;AACH,eAAO,MAAM,MAAM,EAAE,SAAS,eAAe,EAQ5C,CAAC"}
+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../../src/core/checks/manifest.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAElD;;;GAGG;AACH,eAAO,MAAM,MAAM,EAAE,SAAS,eAAe,EAS5C,CAAC"}

package/dist/core/checks/manifest.js

@@ -1,5 +1,6 @@
 import { CATALOG_CHECKS } from './catalog-checks.js';
 import { DISCLOSURE_CHECKS } from './disclosure-checks.js';
+import { HARNESS_PORTABILITY_CHECKS } from './harness-portability-checks.js';
 import { INTEGRITY_CHECKS } from './integrity-checks.js';
 import { failClosedVisibilityCheck, failClosedVisibilityInvariantCheck } from '../notes/checks.js';
 import { ORGANIZE_CHECKS } from './organize-checks.js';
@@ -16,5 +17,6 @@ export const CHECKS = [
     ...ORGANIZE_CHECKS,
     ...DISCLOSURE_CHECKS,
     ...INTEGRITY_CHECKS,
+    ...HARNESS_PORTABILITY_CHECKS,
 ];
 //# sourceMappingURL=manifest.js.map

package/dist/core/checks/manifest.js.map

@@ -1 +1 @@
-{"version":3,"file":"manifest.js","sourceRoot":"","sources":["../../../src/core/checks/manifest.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAC;AAC3D,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,yBAAyB,EAAE,kCAAkC,EAAE,MAAM,oBAAoB,CAAC;AACnG,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAC;AAGrE;;;GAGG;AACH,MAAM,CAAC,MAAM,MAAM,GAA+B;IAChD,yBAAyB;IACzB,kCAAkC;IAClC,GAAG,sBAAsB;IACzB,GAAG,cAAc;IACjB,GAAG,eAAe;IAClB,GAAG,iBAAiB;IACpB,GAAG,gBAAgB;CACpB,CAAC"}
+{"version":3,"file":"manifest.js","sourceRoot":"","sources":["../../../src/core/checks/manifest.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAC;AAC3D,OAAO,EAAE,0BAA0B,EAAE,MAAM,iCAAiC,CAAC;AAC7E,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,yBAAyB,EAAE,kCAAkC,EAAE,MAAM,oBAAoB,CAAC;AACnG,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAC;AAGrE;;;GAGG;AACH,MAAM,CAAC,MAAM,MAAM,GAA+B;IAChD,yBAAyB;IACzB,kCAAkC;IAClC,GAAG,sBAAsB;IACzB,GAAG,cAAc;IACjB,GAAG,eAAe;IAClB,GAAG,iBAAiB;IACpB,GAAG,gBAAgB;IACnB,GAAG,0BAA0B;CAC9B,CAAC"}

package/dist/core/checks/organize-checks.d.ts

@@ -1,6 +1,14 @@
 /** context-organize spec: "orphaned notes" — reported by lint, never failed by doctor. */
 export declare const orphanNotesCheck: import("./types.js").CheckDefinition;
-/** context-organize spec: "broken links" — the graph's dangling links (not_found or ambiguous), reported not failed. Shares detection with the doctor-facing invariant checks/integrity-checks.ts:graphDanglingLinksCheck under a different id (task 9.4: two ids, two severity lanes, one condition, never double-counted within a single run). */
+/**
+ * context-organize spec: "broken links" — a link that resolves to no note at all
+ * (`not_found`), reported not failed. `graph.dangling` also carries `ambiguous`-reason
+ * records (a link matching two or more notes' basenames), but those are
+ * checks/integrity-checks.ts:graphAmbiguousLinksCheck's alone (doctor, invariant): resolution
+ * is mechanically broken there, with an always-applicable fix, unlike a `not_found` link,
+ * which can't be told apart from a healthy forward reference — so this check filters
+ * `ambiguous` out rather than sharing it.
+ */
 export declare const brokenLinksCheck: import("./types.js").CheckDefinition;
 /** context-ingest / context-organize: material captured but never stamped with source identity. */
 export declare const uningestedInboxCheck: import("./types.js").CheckDefinition;
@@ -16,5 +24,17 @@ export declare const uningestedInboxCheck: import("./types.js").CheckDefinition;
 export declare const catalogGapsLintCheck: import("./types.js").CheckDefinition;
 /** context-organize spec (store-primitives-from-migration-audit D4): a rollup with no timestamp, or one whose backlinks have moved past it, reported not failed. */
 export declare const rollupStaleCheck: import("./types.js").CheckDefinition;
+/**
+ * harness-portability spec (inline-conventions-and-mission): "Generated
+ * sections render in a fixed order" — hand-written content interrupting the
+ * managed fences' contiguity blocks `ctxr update` from reordering them to
+ * the fixed layout (`reorderFencedRegions`' own conservative rule: never
+ * relocate content it can't be sure sits outside every managed section).
+ * Reported here as an observation, not by `doctor`: `doctor` runs only
+ * `severity: 'invariant'` checks (`src/commands/doctor.ts`), and a store
+ * whose sections are merely out of the preferred order still functions —
+ * this is exactly the report-don't-block condition lint exists for.
+ */
+export declare const agentsMdSectionOrderBlockedCheck: import("./types.js").CheckDefinition;
 export declare const ORGANIZE_CHECKS: import("./types.js").CheckDefinition[];
 //# sourceMappingURL=organize-checks.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"organize-checks.d.ts","sourceRoot":"","sources":["../../../src/core/checks/organize-checks.ts"],"names":[],"mappings":"AAYA,0FAA0F;AAC1F,eAAO,MAAM,gBAAgB,sCAiB3B,CAAC;AAEH;;;;;;;;GAQG;AACH,eAAO,MAAM,gBAAgB,sCAoB3B,CAAC;AAEH,mGAAmG;AACnG,eAAO,MAAM,oBAAoB,sCAqB/B,CAAC;AAEH;;;;;;;;GAQG;AACH,eAAO,MAAM,oBAAoB,sCAgB/B,CAAC;AAEH,oKAAoK;AACpK,eAAO,MAAM,gBAAgB,sCAqB3B,CAAC;AAEH;;;;;;;;;;GAUG;AACH,eAAO,MAAM,gCAAgC,sCA2B3C,CAAC;AAEH,eAAO,MAAM,eAAe,wCAO3B,CAAC"}