ctxr-cli 0.4.1 → 0.5.0

package/dist/core/conventions.js

@@ -1,5 +1,6 @@
 import { readdir, readFile } from 'node:fs/promises';
 import path from 'node:path';
+import { GENERIC_END_RE, GENERIC_START_RE } from './fs/fenced-region.js';
 import { parseNoteText } from './notes/parse.js';
 const HEADING_RE = /^#\s+(.+)$/m;
 /** The skill-layout filename: `<slug>/SKILL.md` — what harnesses with skill auto-discovery read. */
@@ -27,8 +28,48 @@ export function extractDocMetadata(raw, relativePath) {
             (heading && heading.length > 0 ? heading : undefined) ??
             fallback,
         description: typeof fmDescription === 'string' && fmDescription.length > 0 ? fmDescription : null,
+        body,
     };
 }
+const ATX_HEADING_RE = /^(#{1,6})(\s+.*)$/;
+/**
+ * inline-conventions-and-mission: renders a scanned doc's body for inlining
+ * into a generated `AGENTS.md` section — a leading `# <title>` heading
+ * dropped when it duplicates the section heading the caller already
+ * provides, every remaining ATX heading demoted by `headingOffset` levels
+ * (capped at H6), and any nested `contexture:<region>` fence marker line
+ * stripped (its body kept, only the marker comment removed) so a fence
+ * copied out of a source file — e.g. mission.md's own rollup fence — never
+ * leaves an orphaned marker inside AGENTS.md's fence.
+ */
+export function inlineDocBody(doc, headingOffset) {
+    const lines = doc.body.split('\n');
+    let start = 0;
+    while (start < lines.length && lines[start].trim() === '')
+        start += 1;
+    const firstHeading = start < lines.length ? ATX_HEADING_RE.exec(lines[start]) : null;
+    if (firstHeading && firstHeading[1].length === 1 && firstHeading[2].trim().toLowerCase() === doc.title.trim().toLowerCase()) {
+        start += 1;
+        while (start < lines.length && lines[start].trim() === '')
+            start += 1;
+    }
+    const out = [];
+    for (const line of lines.slice(start)) {
+        if (GENERIC_START_RE.test(line) || GENERIC_END_RE.test(line))
+            continue;
+        const heading = ATX_HEADING_RE.exec(line);
+        if (heading) {
+            const level = Math.min(heading[1].length + headingOffset, 6);
+            out.push(`${'#'.repeat(level)}${heading[2]}`);
+        }
+        else {
+            out.push(line);
+        }
+    }
+    while (out.length > 0 && out[out.length - 1].trim() === '')
+        out.pop();
+    return out;
+}
 export async function scanDocsDir(root, dirRelativePath) {
     const dir = path.join(root, dirRelativePath);
     let entries;
@@ -66,8 +107,29 @@ export async function scanDocsDir(root, dirRelativePath) {
     }
     return docs;
 }
-/** Every operator convention doc currently at the configured path. */
-export function scanConventions(root, config) {
-    return scanDocsDir(root, config.harness.conventions_path);
+/**
+ * compose-store-guidance-documents: the mission document, when configured,
+ * commonly lives in the same guidance directory as convention files (its
+ * shipped default is `<guidance_path>/mission.md`) but is never itself a
+ * convention — it already gets its own "Mission" section
+ * (inline-conventions-and-mission's `renderMissionSection`). Excluded by
+ * basename so inlining conventions never double-renders it.
+ */
+function reservedGuidanceFileNames(config) {
+    const names = new Set();
+    if (config.organize.mission_path)
+        names.add(path.basename(config.organize.mission_path));
+    return names;
+}
+/**
+ * Every convention doc currently at the configured guidance path —
+ * contexture's own shipped baseline (see `templates/conventions/baseline-convention.md`,
+ * synced by `syncBaselineConvention` in `convention-doc.ts`) alongside
+ * whatever the operator has added — minus the mission document.
+ */
+export async function scanConventions(root, config) {
+    const docs = await scanDocsDir(root, config.harness.guidance_path);
+    const reserved = reservedGuidanceFileNames(config);
+    return docs.filter((doc) => !reserved.has(path.basename(doc.path)));
 }
 //# sourceMappingURL=conventions.js.map

package/dist/core/conventions.js.map

@@ -1 +1 @@
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package/dist/core/fs/fenced-region.d.ts

@@ -63,6 +63,44 @@ export declare function removeFencedRegion(text: string, fence: Fence): UpsertFe
 export declare function removeFencedRegionFromFile(filePath: string, fence: Fence): Promise<{
     changed: boolean;
 }>;
+export interface FenceSpan {
+    fence: Fence;
+    startIdx: number;
+    endIdx: number;
+}
+export interface ReorderFencedRegionsResult {
+    text: string;
+    changed: boolean;
+    /** True when the fences present are not all separated by blank lines only — no change was made. */
+    blocked: boolean;
+}
+/**
+ * inline-conventions-and-mission (design.md "Reordering is opt-in-safe"):
+ * moves every fence from `orderedFences` that is present in `text` to match
+ * that order, but ONLY when every present fence is separated from its
+ * neighbor (in the file's current order) by nothing but blank lines — the
+ * conservative reading of "never silently relocate hand-written content
+ * relative to sections it was written to sit near." Each fence's own body is
+ * moved byte-for-byte; content before the first present fence and after the
+ * last is untouched. A fence from `orderedFences` absent from `text` is
+ * skipped, not an error. Fewer than two fences present is a no-op (nothing
+ * to reorder), and matching order already is `changed: false`.
+ */
+export declare function reorderFencedRegions(text: string, orderedFences: readonly Fence[]): ReorderFencedRegionsResult;
+/** File-backed counterpart to `reorderFencedRegions` — a missing file has nothing to reorder. */
+export declare function reorderFencedRegionsInFile(filePath: string, orderedFences: readonly Fence[]): Promise<{
+    changed: boolean;
+    blocked: boolean;
+}>;
+/**
+ * Comment-syntax-agnostic fence-marker detection, shared with `inlineDocBody`
+ * (`conventions.ts`) so a nested `contexture:<region>` fence copied out of a
+ * source file (e.g. a rollup fence inside a mission document) is stripped by
+ * the exact same rule `validateFenceIntegrity` uses to find one, rather than
+ * a second regex that could quietly drift from it.
+ */
+export declare const GENERIC_START_RE: RegExp;
+export declare const GENERIC_END_RE: RegExp;
 /**
  * Pure validation, comment-syntax-agnostic (matches the `contexture:<region>`
  * token regardless of whether it's wrapped in `#`, `<!-- -->`, or anything

package/dist/core/fs/fenced-region.d.ts.map

@@ -1 +1 @@
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package/dist/core/fs/fenced-region.js

@@ -184,8 +184,94 @@ export async function removeFencedRegionFromFile(filePath, fence) {
     }
     return { changed: result.changed };
 }
-const GENERIC_START_RE = />>>\s*contexture:(\S+)/;
-const GENERIC_END_RE = /<<<\s*contexture:(\S+)/;
+function locateFence(lines, fence) {
+    const startIndices = indicesOf(lines, fence.start);
+    const endIndices = indicesOf(lines, fence.end);
+    if (startIndices.length === 0 && endIndices.length === 0)
+        return null;
+    if (startIndices.length === 1 && endIndices.length === 1 && startIndices[0] < endIndices[0]) {
+        return { fence, startIdx: startIndices[0], endIdx: endIndices[0] };
+    }
+    throw new FenceMismatch(`found ${startIndices.length} start marker(s) and ${endIndices.length} end marker(s) while reordering`);
+}
+/**
+ * inline-conventions-and-mission (design.md "Reordering is opt-in-safe"):
+ * moves every fence from `orderedFences` that is present in `text` to match
+ * that order, but ONLY when every present fence is separated from its
+ * neighbor (in the file's current order) by nothing but blank lines — the
+ * conservative reading of "never silently relocate hand-written content
+ * relative to sections it was written to sit near." Each fence's own body is
+ * moved byte-for-byte; content before the first present fence and after the
+ * last is untouched. A fence from `orderedFences` absent from `text` is
+ * skipped, not an error. Fewer than two fences present is a no-op (nothing
+ * to reorder), and matching order already is `changed: false`.
+ */
+export function reorderFencedRegions(text, orderedFences) {
+    const trailingNewline = text.endsWith('\n');
+    const lines = text.length === 0 ? [] : text.split('\n');
+    if (trailingNewline)
+        lines.pop();
+    const desiredOrder = [];
+    for (const fence of orderedFences) {
+        const span = locateFence(lines, fence);
+        if (span)
+            desiredOrder.push(span);
+    }
+    if (desiredOrder.length < 2) {
+        return { text, changed: false, blocked: false };
+    }
+    const byFileOrder = [...desiredOrder].sort((a, b) => a.startIdx - b.startIdx);
+    for (let i = 0; i < byFileOrder.length - 1; i += 1) {
+        const gapStart = byFileOrder[i].endIdx + 1;
+        const gapEnd = byFileOrder[i + 1].startIdx;
+        for (let j = gapStart; j < gapEnd; j += 1) {
+            if (lines[j] !== '') {
+                return { text, changed: false, blocked: true };
+            }
+        }
+    }
+    const alreadyInOrder = byFileOrder.every((span, i) => span.fence === desiredOrder[i].fence);
+    if (alreadyInOrder) {
+        return { text, changed: false, blocked: false };
+    }
+    const before = lines.slice(0, byFileOrder[0].startIdx);
+    const after = lines.slice(byFileOrder[byFileOrder.length - 1].endIdx + 1);
+    const rebuilt = [...before];
+    for (const [i, span] of desiredOrder.entries()) {
+        if (i > 0)
+            rebuilt.push('');
+        rebuilt.push(...lines.slice(span.startIdx, span.endIdx + 1));
+    }
+    rebuilt.push(...after);
+    const result = finish(rebuilt, text);
+    return { ...result, blocked: false };
+}
+/** File-backed counterpart to `reorderFencedRegions` — a missing file has nothing to reorder. */
+export async function reorderFencedRegionsInFile(filePath, orderedFences) {
+    let existing = '';
+    try {
+        existing = await readFile(filePath, 'utf8');
+    }
+    catch (err) {
+        if (err.code !== 'ENOENT')
+            throw err;
+        return { changed: false, blocked: false };
+    }
+    const result = reorderFencedRegions(existing, orderedFences);
+    if (result.changed) {
+        await writeFileAtomic(filePath, result.text);
+    }
+    return { changed: result.changed, blocked: result.blocked };
+}
+/**
+ * Comment-syntax-agnostic fence-marker detection, shared with `inlineDocBody`
+ * (`conventions.ts`) so a nested `contexture:<region>` fence copied out of a
+ * source file (e.g. a rollup fence inside a mission document) is stripped by
+ * the exact same rule `validateFenceIntegrity` uses to find one, rather than
+ * a second regex that could quietly drift from it.
+ */
+export const GENERIC_START_RE = />>>\s*contexture:(\S+)/;
+export const GENERIC_END_RE = /<<<\s*contexture:(\S+)/;
 /**
  * Pure validation, comment-syntax-agnostic (matches the `contexture:<region>`
  * token regardless of whether it's wrapped in `#`, `<!-- -->`, or anything

package/dist/core/fs/fenced-region.js.map

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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":"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"}
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/core/migrations/registry.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAE5C,gHAAgH;AAChH,eAAO,MAAM,UAAU,EAAE,SAAS,SAAS,EAI1C,CAAC;AAEF,qHAAqH;AACrH,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG,SAAS,EAAE,CAElE"}

package/dist/core/migrations/registry.js

@@ -1,7 +1,12 @@
+import { renameConventionsPathMigration } from './rename-conventions-path.js';
 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, renameProceduresPathMigration];
+export const MIGRATIONS = [
+    renameVisibilityFieldMigration,
+    renameProceduresPathMigration,
+    renameConventionsPathMigration,
+];
 /** 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 @@
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+{"version":3,"file":"registry.js","sourceRoot":"","sources":["../../../src/core/migrations/registry.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,8BAA8B,EAAE,MAAM,8BAA8B,CAAC;AAC9E,OAAO,EAAE,6BAA6B,EAAE,MAAM,6BAA6B,CAAC;AAC5E,OAAO,EAAE,8BAA8B,EAAE,MAAM,8BAA8B,CAAC;AAG9E,gHAAgH;AAChH,MAAM,CAAC,MAAM,UAAU,GAAyB;IAC9C,8BAA8B;IAC9B,6BAA6B;IAC7B,8BAA8B;CAC/B,CAAC;AAEF,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-conventions-path.d.ts

@@ -0,0 +1,26 @@
+import type { Migration } from './types.js';
+/**
+ * rename-conventions-path-to-guidance-path (compose-store-guidance-documents
+ * design.md D1/D7): unlike 0003's pure key rename, the key's *default value*
+ * also changes (`.contexture/conventions/` -> `.contexture/guidance/`), so a
+ * store that never customized the path needs its directory moved on disk,
+ * not merely its config key renamed. An operator-customized path is left
+ * exactly where it is — only the key spelling changes for them.
+ *
+ * Migrations only see `Store` (`root` + `config`, no `GitRunner` — see
+ * core/store.ts), so the directory move is a plain filesystem rename, not
+ * `git mv`. History is still preserved: whatever commits this migration's
+ * output (the normal session-submit flow) stages a coherent delete-old,
+ * add-new diff, which `git log --follow`'s content-similarity rename
+ * detection recognizes identically to an explicit `git mv` — git never
+ * records "this was a rename" as a distinct fact in its object model
+ * either way.
+ *
+ * Pending-ness is `store.config.schema_version < 4`, the same
+ * schema-version-not-key-presence rule 0003 established, for the same
+ * reason: `HarnessSchema`'s fallback transform already populates
+ * `guidance_path` on an unmigrated store, so its presence can't distinguish
+ * migrated from not.
+ */
+export declare const renameConventionsPathMigration: Migration;
+//# sourceMappingURL=rename-conventions-path.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"rename-conventions-path.d.ts","sourceRoot":"","sources":["../../../src/core/migrations/rename-conventions-path.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,SAAS,EAAkB,MAAM,YAAY,CAAC;AAiB5D;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,eAAO,MAAM,8BAA8B,EAAE,SA+C5C,CAAC"}

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

@@ -0,0 +1,86 @@
+import { existsSync } from 'node:fs';
+import { rename } from 'node:fs/promises';
+import path from 'node:path';
+import { readConfig } from '../../config/load.js';
+import { renderStoreConfig } from '../../config/render.js';
+import { writeFileAtomic } from '../fs/atomic.js';
+const OLD_DEFAULT_GUIDANCE_PATH = '.contexture/conventions/';
+const NEW_DEFAULT_GUIDANCE_PATH = '.contexture/guidance/';
+const CONFIG_DELTA = {
+    path: 'contexture.yaml',
+    description: 'rename harness.conventions_path to harness.guidance_path and set schema_version to 4',
+};
+function directoryDelta() {
+    return {
+        path: NEW_DEFAULT_GUIDANCE_PATH,
+        description: `move the default-valued guidance directory from ${OLD_DEFAULT_GUIDANCE_PATH} to ${NEW_DEFAULT_GUIDANCE_PATH}`,
+    };
+}
+/**
+ * rename-conventions-path-to-guidance-path (compose-store-guidance-documents
+ * design.md D1/D7): unlike 0003's pure key rename, the key's *default value*
+ * also changes (`.contexture/conventions/` -> `.contexture/guidance/`), so a
+ * store that never customized the path needs its directory moved on disk,
+ * not merely its config key renamed. An operator-customized path is left
+ * exactly where it is — only the key spelling changes for them.
+ *
+ * Migrations only see `Store` (`root` + `config`, no `GitRunner` — see
+ * core/store.ts), so the directory move is a plain filesystem rename, not
+ * `git mv`. History is still preserved: whatever commits this migration's
+ * output (the normal session-submit flow) stages a coherent delete-old,
+ * add-new diff, which `git log --follow`'s content-similarity rename
+ * detection recognizes identically to an explicit `git mv` — git never
+ * records "this was a rename" as a distinct fact in its object model
+ * either way.
+ *
+ * Pending-ness is `store.config.schema_version < 4`, the same
+ * schema-version-not-key-presence rule 0003 established, for the same
+ * reason: `HarnessSchema`'s fallback transform already populates
+ * `guidance_path` on an unmigrated store, so its presence can't distinguish
+ * migrated from not.
+ */
+export const renameConventionsPathMigration = {
+    id: '0004-rename-conventions-path-to-guidance-path',
+    fromVersion: 3,
+    toVersion: 4,
+    description: 'Rename the harness.conventions_path config key to harness.guidance_path, move the guidance directory when it sat at the old default, and bump schema_version to 4.',
+    async plan(store) {
+        if (store.config.schema_version >= 4)
+            return [];
+        const deltas = [CONFIG_DELTA];
+        if (store.config.harness.guidance_path === OLD_DEFAULT_GUIDANCE_PATH)
+            deltas.push(directoryDelta());
+        return deltas;
+    },
+    async apply(store) {
+        if (store.config.schema_version >= 4)
+            return [];
+        const configPath = path.join(store.root, 'contexture.yaml');
+        // readConfig() already resolves harness.guidance_path via HarnessSchema's
+        // fallback (from conventions_path if that's all the file has), so
+        // currentConfig.harness carries no conventions_path key at all —
+        // rendering it below writes only guidance_path to disk.
+        const currentConfig = await readConfig(store.root);
+        const appliedDeltas = [CONFIG_DELTA];
+        let guidancePath = currentConfig.harness.guidance_path;
+        if (guidancePath === OLD_DEFAULT_GUIDANCE_PATH) {
+            const oldDir = path.join(store.root, OLD_DEFAULT_GUIDANCE_PATH);
+            const newDir = path.join(store.root, NEW_DEFAULT_GUIDANCE_PATH);
+            // Absent when the store never carried any convention files — nothing
+            // to move on disk, only the config value changes.
+            if (existsSync(oldDir)) {
+                await rename(oldDir, newDir);
+            }
+            guidancePath = NEW_DEFAULT_GUIDANCE_PATH;
+            appliedDeltas.push(directoryDelta());
+        }
+        const nextConfig = {
+            ...currentConfig,
+            schema_version: 4,
+            harness: { ...currentConfig.harness, guidance_path: guidancePath },
+        };
+        await writeFileAtomic(configPath, renderStoreConfig(nextConfig));
+        return appliedDeltas;
+    },
+};
+//# sourceMappingURL=rename-conventions-path.js.map

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

@@ -0,0 +1 @@
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package/dist/core/notes/list.js

@@ -41,9 +41,9 @@ export function excludedPrefixesFor(config) {
         ...config.derived.paths,
         config.session.worktrees_path,
         config.catalog.path,
-        // Tool-owned instruction docs (skills, conventions) are never notes, wherever they live.
+        // Tool-owned instruction docs (skills, guidance) are never notes, wherever they live.
         config.harness.skills_path,
-        config.harness.conventions_path,
+        config.harness.guidance_path,
     ];
 }
 async function walk(dir, root, excludePrefixes, skipRootFiles, results) {

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

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

@@ -1 +1 @@
-{"version":3,"file":"reconcile.d.ts","sourceRoot":"","sources":["../../src/core/reconcile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AACvD,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,UAAU,CAAC;AAcvC,eAAO,MAAM,yBAAyB,8BAA4B,CAAC;AAanE,MAAM,WAAW,eAAe;IAC9B,+EAA+E;IAC/E,OAAO,EAAE,MAAM,EAAE,CAAC;CACnB;AAED;;;;;;;GAOG;AACH,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,eAAe,CAAC,CAmC7G"}
+{"version":3,"file":"reconcile.d.ts","sourceRoot":"","sources":["../../src/core/reconcile.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AACvD,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,UAAU,CAAC;AAiBvC,eAAO,MAAM,yBAAyB,8BAA4B,CAAC;AAwBnE,MAAM,WAAW,eAAe;IAC9B,+EAA+E;IAC/E,OAAO,EAAE,MAAM,EAAE,CAAC;CACnB;AAED;;;;;;;GAOG;AACH,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,eAAe,CAAC,CAoD7G"}

package/dist/core/reconcile.js

@@ -1,6 +1,8 @@
 import path from 'node:path';
-import { agentsMdPath, buildAgentsCanonicalSection, buildAgentsCaptureSection, buildAgentsConventionsSection, buildAgentsLegRoutingSection, buildAgentsPlacementSection, } from './agents-doc.js';
-import { removeFencedRegionFromFile, upsertFencedRegionInFile } from './fs/fenced-region.js';
+import { DEFAULT_BASELINE_CONVENTION_FILE_NAME } from '../config/defaults.js';
+import { agentsMdPath, AGENTS_MD_SECTION_ORDER, buildAgentsCanonicalSection, buildAgentsCaptureSection, buildAgentsConventionsSection, buildAgentsLegRoutingSection, buildAgentsMissionSection, buildAgentsPlacementSection, } from './agents-doc.js';
+import { syncBaselineConvention } from './convention-doc.js';
+import { removeFencedRegionFromFile, reorderFencedRegionsInFile, upsertFencedRegionInFile } from './fs/fenced-region.js';
 import { configureHooksPath, installHooks } from './hooks.js';
 import { commentFence, DERIVED_GITIGNORE_FENCE, htmlCommentFence } from './markers.js';
 import { syncShippedSkills } from './skills.js';
@@ -15,6 +17,16 @@ export const WORKTREES_GITIGNORE_FENCE = commentFence('worktrees');
  * contexture issue #14 tracks.
  */
 const RETIRED_AGENTS_MD_IDENTITY_FENCE = htmlCommentFence('agent-identity');
+/**
+ * compose-store-guidance-documents: the conventions fence was renamed from
+ * `store-conventions` to `conventions` (dropping the redundant "store-"
+ * prefix — every sibling fence/template already omits it, e.g. `canonical`,
+ * `placement`, `mission`). Same one-time cleanup shape as the identity
+ * retirement above: `buildAgentsConventionsSection` already writes the new
+ * `contexture:conventions` fence via the loop below, so this only needs to
+ * remove the orphaned old one.
+ */
+const RETIRED_AGENTS_MD_STORE_CONVENTIONS_FENCE = htmlCommentFence('store-conventions');
 /**
  * Brings every contexture-OWNED file in a store to the installed package's
  * version: the managed .gitignore blocks, every generated AGENTS.md
@@ -32,15 +44,22 @@ export async function reconcileStore(env, root, config) {
     const gitignorePath = path.join(root, '.gitignore');
     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 skill index is a disk scan.
+    // The owned skill copies are refreshed unconditionally here — not because
+    // any AGENTS.md section reads them anymore (inline-conventions-and-mission
+    // removed the skill index), but because init/update must still deliver
+    // the skill files to disk regardless of what AGENTS.md renders.
     changed.push(...(await syncShippedSkills(root, config)));
+    // Same reason, same ordering constraint as skills: the shipped baseline
+    // convention file must be current on disk BEFORE buildAgentsConventionsSection
+    // scans the guidance directory and inlines it (compose-store-guidance-documents).
+    note(path.join(config.harness.guidance_path, DEFAULT_BASELINE_CONVENTION_FILE_NAME).split(path.sep).join('/'), (await syncBaselineConvention(root, config)).changed);
     let agentsChanged = false;
     for (const build of [
         buildAgentsLegRoutingSection,
         buildAgentsCaptureSection,
         buildAgentsPlacementSection,
         buildAgentsCanonicalSection,
+        buildAgentsMissionSection,
         buildAgentsConventionsSection,
     ]) {
         if ((await build(root, config)).changed)
@@ -48,6 +67,14 @@ export async function reconcileStore(env, root, config) {
     }
     if ((await removeFencedRegionFromFile(agentsMdPath(root), RETIRED_AGENTS_MD_IDENTITY_FENCE)).changed)
         agentsChanged = true;
+    if ((await removeFencedRegionFromFile(agentsMdPath(root), RETIRED_AGENTS_MD_STORE_CONVENTIONS_FENCE)).changed)
+        agentsChanged = true;
+    // harness-portability spec "Generated sections render in a fixed order":
+    // reorders once every section fence above has been written/refreshed, so
+    // a first-time init and a subsequent update converge on the same layout.
+    // A no-op when the fences aren't all contiguous — see `reorderFencedRegions`.
+    if ((await reorderFencedRegionsInFile(agentsMdPath(root), AGENTS_MD_SECTION_ORDER)).changed)
+        agentsChanged = true;
     note('AGENTS.md', agentsChanged);
     const { changed: hookFiles } = await installHooks(root, config.git.default_branch);
     changed.push(...hookFiles);

package/dist/core/reconcile.js.map

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package/dist/core/rollup.d.ts

@@ -35,8 +35,8 @@ export declare function checkRollupStaleness(git: GitRunner, root: string, entit
 export declare function checkMissionStaleness(note: Note, staleDays: number, now: Date): StaleRollupEntry | null;
 /**
  * Every entity with a rollup section (optionally narrowed to one), reported
- * stale per `checkRollupStaleness`, plus — when `missionPath` names a note
- * that exists in `notes` — that one path via `checkMissionStaleness`
+ * stale per `checkRollupStaleness`, plus — when `missionPath` names a
+ * document that exists on disk — that one path via `checkMissionStaleness`
  * instead of the backlink-based entity scan, even when it carries no
  * `ROLLUP_FENCE` yet (an unwritten mission document must surface as
  * needing its first write, not be silently excluded by `hasRollupSection`).

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

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