ctxr-cli 0.1.0

package/dist/core/notes/checks.d.ts

@@ -0,0 +1,20 @@
+/**
+ * store-lifecycle/context-visibility: a note relying on the fail-closed
+ * default is a health OBSERVATION (lint), not a doctor-failing invariant —
+ * doctor's own fail-closed-visibility invariant (wired in Phase 5, below)
+ * is a different, stricter check. `severity: 'observation'` is what keeps
+ * this out of doctor's exit code by construction, via the same registry
+ * lint reads from in Phase 7.
+ */
+export declare const failClosedVisibilityCheck: import("../checks/types.js").CheckDefinition;
+/**
+ * context-visibility spec (task 5.2): the same underlying condition as the
+ * lint-facing observation above, registered a second time as its own
+ * invariant so `doctor` can fail a run on it. Each check id carries exactly
+ * one severity, so the two never double-count a single run's pass/fail
+ * totals against each other (task 9.4) even though both watch the same
+ * condition for two different audiences (an operator skimming lint output,
+ * versus a gate that must block).
+ */
+export declare const failClosedVisibilityInvariantCheck: import("../checks/types.js").CheckDefinition;
+//# sourceMappingURL=checks.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"checks.d.ts","sourceRoot":"","sources":["../../../src/core/notes/checks.ts"],"names":[],"mappings":"AAsBA;;;;;;;GAOG;AACH,eAAO,MAAM,yBAAyB,8CAUpC,CAAC;AAEH;;;;;;;;GAQG;AACH,eAAO,MAAM,kCAAkC,8CAU7C,CAAC"}

package/dist/core/notes/checks.js

@@ -0,0 +1,58 @@
+import { defineCheck } from '../checks/types.js';
+import { resolveVisibility } from './visibility.js';
+async function failClosedFindings(ctx) {
+    const notes = await ctx.notes();
+    const findings = [];
+    for (const note of notes) {
+        const resolution = resolveVisibility(ctx.config, note);
+        if (resolution.reason === 'fail-closed default') {
+            findings.push({
+                code: 'visibility.fail_closed_default',
+                severity: 'info',
+                message: `"${note.path}" has no explicit or directory-derived visibility; relying on the fail-closed default.`,
+                subject: note.path,
+            });
+        }
+    }
+    return findings;
+}
+/**
+ * store-lifecycle/context-visibility: a note relying on the fail-closed
+ * default is a health OBSERVATION (lint), not a doctor-failing invariant —
+ * doctor's own fail-closed-visibility invariant (wired in Phase 5, below)
+ * is a different, stricter check. `severity: 'observation'` is what keeps
+ * this out of doctor's exit code by construction, via the same registry
+ * lint reads from in Phase 7.
+ */
+export const failClosedVisibilityCheck = defineCheck({
+    id: 'visibility.fail_closed_default',
+    title: 'Notes relying on the fail-closed default visibility',
+    severity: 'observation',
+    capability: 'context-visibility',
+    scopes: ['store'],
+    async run(ctx) {
+        const findings = await failClosedFindings(ctx);
+        return { status: findings.length > 0 ? 'fail' : 'pass', findings };
+    },
+});
+/**
+ * context-visibility spec (task 5.2): the same underlying condition as the
+ * lint-facing observation above, registered a second time as its own
+ * invariant so `doctor` can fail a run on it. Each check id carries exactly
+ * one severity, so the two never double-count a single run's pass/fail
+ * totals against each other (task 9.4) even though both watch the same
+ * condition for two different audiences (an operator skimming lint output,
+ * versus a gate that must block).
+ */
+export const failClosedVisibilityInvariantCheck = defineCheck({
+    id: 'visibility.fail_closed_default_invariant',
+    title: 'Every note has a resolvable visibility value',
+    severity: 'invariant',
+    capability: 'context-visibility',
+    scopes: ['store'],
+    async run(ctx) {
+        const findings = await failClosedFindings(ctx);
+        return { status: findings.length > 0 ? 'fail' : 'pass', findings };
+    },
+});
+//# sourceMappingURL=checks.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"checks.js","sourceRoot":"","sources":["../../../src/core/notes/checks.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AAEpD,KAAK,UAAU,kBAAkB,CAAC,GAAiB;IACjD,MAAM,KAAK,GAAG,MAAM,GAAG,CAAC,KAAK,EAAE,CAAC;IAChC,MAAM,QAAQ,GAAc,EAAE,CAAC;IAC/B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,UAAU,GAAG,iBAAiB,CAAC,GAAG,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;QACvD,IAAI,UAAU,CAAC,MAAM,KAAK,qBAAqB,EAAE,CAAC;YAChD,QAAQ,CAAC,IAAI,CAAC;gBACZ,IAAI,EAAE,gCAAgC;gBACtC,QAAQ,EAAE,MAAM;gBAChB,OAAO,EAAE,IAAI,IAAI,CAAC,IAAI,wFAAwF;gBAC9G,OAAO,EAAE,IAAI,CAAC,IAAI;aACnB,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,CAAC,MAAM,yBAAyB,GAAG,WAAW,CAAC;IACnD,EAAE,EAAE,gCAAgC;IACpC,KAAK,EAAE,qDAAqD;IAC5D,QAAQ,EAAE,aAAa;IACvB,UAAU,EAAE,oBAAoB;IAChC,MAAM,EAAE,CAAC,OAAO,CAAC;IACjB,KAAK,CAAC,GAAG,CAAC,GAAG;QACX,MAAM,QAAQ,GAAG,MAAM,kBAAkB,CAAC,GAAG,CAAC,CAAC;QAC/C,OAAO,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,QAAQ,EAAE,CAAC;IACrE,CAAC;CACF,CAAC,CAAC;AAEH;;;;;;;;GAQG;AACH,MAAM,CAAC,MAAM,kCAAkC,GAAG,WAAW,CAAC;IAC5D,EAAE,EAAE,0CAA0C;IAC9C,KAAK,EAAE,8CAA8C;IACrD,QAAQ,EAAE,WAAW;IACrB,UAAU,EAAE,oBAAoB;IAChC,MAAM,EAAE,CAAC,OAAO,CAAC;IACjB,KAAK,CAAC,GAAG,CAAC,GAAG;QACX,MAAM,QAAQ,GAAG,MAAM,kBAAkB,CAAC,GAAG,CAAC,CAAC;QAC/C,OAAO,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,QAAQ,EAAE,CAAC;IACrE,CAAC;CACF,CAAC,CAAC"}

package/dist/core/notes/list.d.ts

@@ -0,0 +1,26 @@
+import type { StoreConfig } from '../../config/schema.js';
+/**
+ * The note-enumeration seam every later retrieval leg builds on. `as` is
+ * accepted (and, until Phase 5, ignored) from Phase 0 — a real finding:
+ * openspec/config.yaml's own authoring rule says "sequence visibility
+ * enforcement before retrieval — a pre-filter cannot be safely retrofitted
+ * from a post-filter," but tasks.md's phase order puts retrieval (Phase 3/4)
+ * before visibility enforcement (Phase 5). Accepting `as` here from the
+ * start means Phase 5 wires a real filter into an already-filterable
+ * signature, instead of auditing every earlier traversal for safety.
+ */
+export interface NoteQuery {
+    /** The requesting context, for visibility filtering. Wired in Phase 5. */
+    as?: string;
+    underPrefix?: string;
+}
+export interface Note {
+    /** Path relative to the store root, forward-slash separated. */
+    path: string;
+    frontmatter: Record<string, unknown> | undefined;
+    body: string;
+}
+export declare function excludedPrefixesFor(config: StoreConfig): string[];
+/** Every retrievable note in the store: everything under a .md path, minus every declared exclusion. */
+export declare function listNotes(storeRoot: string, config: StoreConfig, query?: NoteQuery): Promise<Note[]>;
+//# sourceMappingURL=list.d.ts.map

package/dist/core/notes/list.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../../src/core/notes/list.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAG1D;;;;;;;;;GASG;AACH,MAAM,WAAW,SAAS;IACxB,0EAA0E;IAC1E,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,IAAI;IACnB,gEAAgE;IAChE,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,SAAS,CAAC;IACjD,IAAI,EAAE,MAAM,CAAC;CACd;AAkCD,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,EAAE,CAUjE;AAkCD,wGAAwG;AACxG,wBAAsB,SAAS,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,KAAK,GAAE,SAAc,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,CAO9G"}

package/dist/core/notes/list.js

@@ -0,0 +1,84 @@
+import { readdir } from 'node:fs/promises';
+import path from 'node:path';
+import { configuredAdapters } from '../../adapters/registry.js';
+import { parseNote } from './parse.js';
+/** Infrastructure directories intrinsic to contexture itself — never configurable content locations. */
+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; without this it would otherwise be
+ * picked up as one, since it lives at the store root as a plain .md file.
+ */
+const ALWAYS_SKIP_FILES = new Set(['AGENTS.md']);
+/**
+ * Root-level files owned by configured harness-generation adapters (e.g.
+ * CLAUDE.md) are tool-owned pointers, never notes. A misconfigured adapter
+ * is doctor's problem to report (adapters.compatibility) — enumeration
+ * must not fail because of it, so resolution errors just skip nothing extra.
+ */
+function harnessEntryFiles(config) {
+    try {
+        return new Set(configuredAdapters(config, 'harness-generation').map((a) => a.entryFileName));
+    }
+    catch {
+        return new Set();
+    }
+}
+function isUnderAnyPrefix(relativePath, prefixes) {
+    return prefixes.some((prefix) => {
+        const trimmed = prefix.replace(/\/+$/, '');
+        return relativePath === trimmed || relativePath.startsWith(`${trimmed}/`);
+    });
+}
+export function excludedPrefixesFor(config) {
+    return [
+        ...config.retrieval.exclude_paths,
+        ...config.derived.paths,
+        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.conventions_path,
+    ];
+}
+async function walk(dir, root, excludePrefixes, skipRootFiles, results) {
+    let entries;
+    try {
+        entries = await readdir(dir, { withFileTypes: true });
+    }
+    catch (err) {
+        if (err.code === 'ENOENT')
+            return;
+        throw err;
+    }
+    for (const entry of entries) {
+        const fullPath = path.join(dir, entry.name);
+        const relativePath = path.relative(root, fullPath).split(path.sep).join('/');
+        if (entry.isDirectory()) {
+            if (ALWAYS_SKIP_DIRS.has(entry.name))
+                continue;
+            if (isUnderAnyPrefix(relativePath, excludePrefixes))
+                continue;
+            await walk(fullPath, root, excludePrefixes, skipRootFiles, results);
+        }
+        else if (entry.isFile() && entry.name.endsWith('.md')) {
+            if (ALWAYS_SKIP_FILES.has(entry.name))
+                continue;
+            if (relativePath === entry.name && skipRootFiles.has(entry.name))
+                continue;
+            if (isUnderAnyPrefix(relativePath, excludePrefixes))
+                continue;
+            results.push(relativePath);
+        }
+    }
+}
+/** Every retrievable note in the store: everything under a .md path, minus every declared exclusion. */
+export async function listNotes(storeRoot, config, query = {}) {
+    const relativePaths = [];
+    await walk(storeRoot, storeRoot, excludedPrefixesFor(config), harnessEntryFiles(config), relativePaths);
+    relativePaths.sort();
+    const scoped = query.underPrefix ? relativePaths.filter((p) => isUnderAnyPrefix(p, [query.underPrefix])) : relativePaths;
+    return Promise.all(scoped.map((relativePath) => parseNote(path.join(storeRoot, relativePath), relativePath)));
+}
+//# sourceMappingURL=list.js.map

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

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

@@ -0,0 +1,12 @@
+import type { Note } from './list.js';
+/**
+ * context-store spec: "A note SHALL be a markdown file whose optional YAML
+ * frontmatter may declare... A note with no frontmatter SHALL be treated as
+ * valid content." Absence of frontmatter is fine; a `---` block that IS
+ * present but fails to parse, or doesn't parse to a mapping, is a real
+ * error — fail loud rather than silently treat malformed content as if it
+ * had no frontmatter at all.
+ */
+export declare function parseNoteText(raw: string, relativePath: string): Note;
+export declare function parseNote(absolutePath: string, relativePath: string): Promise<Note>;
+//# sourceMappingURL=parse.d.ts.map

package/dist/core/notes/parse.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../../src/core/notes/parse.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAItC;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,IAAI,CAqBrE;AAED,wBAAsB,SAAS,CAAC,YAAY,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAGzF"}

package/dist/core/notes/parse.js

@@ -0,0 +1,36 @@
+import { readFile } from 'node:fs/promises';
+import { parse as parseYaml } from 'yaml';
+import { InvalidNoteFrontmatterError } from '../errors.js';
+const FRONTMATTER_RE = /^---\r?\n([\s\S]*?)\r?\n---\r?\n?/;
+/**
+ * context-store spec: "A note SHALL be a markdown file whose optional YAML
+ * frontmatter may declare... A note with no frontmatter SHALL be treated as
+ * valid content." Absence of frontmatter is fine; a `---` block that IS
+ * present but fails to parse, or doesn't parse to a mapping, is a real
+ * error — fail loud rather than silently treat malformed content as if it
+ * had no frontmatter at all.
+ */
+export function parseNoteText(raw, relativePath) {
+    const match = FRONTMATTER_RE.exec(raw);
+    if (!match) {
+        return { path: relativePath, frontmatter: undefined, body: raw };
+    }
+    const frontmatterText = match[1] ?? '';
+    const body = raw.slice(match[0].length);
+    let parsed;
+    try {
+        parsed = parseYaml(frontmatterText);
+    }
+    catch (err) {
+        throw new InvalidNoteFrontmatterError(relativePath, err instanceof Error ? err.message : String(err));
+    }
+    if (parsed === null || typeof parsed !== 'object' || Array.isArray(parsed)) {
+        throw new InvalidNoteFrontmatterError(relativePath, 'frontmatter must be a YAML mapping');
+    }
+    return { path: relativePath, frontmatter: parsed, body };
+}
+export async function parseNote(absolutePath, relativePath) {
+    const raw = await readFile(absolutePath, 'utf8');
+    return parseNoteText(raw, relativePath);
+}
+//# sourceMappingURL=parse.js.map

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

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

@@ -0,0 +1,7 @@
+/**
+ * The inverse of parseNoteText (core/notes/parse.ts): re-serializes a note
+ * back to raw file text. `undefined` frontmatter renders as no frontmatter
+ * block at all, matching parseNoteText's own treatment of absence.
+ */
+export declare function renderNoteText(frontmatter: Record<string, unknown> | undefined, body: string): string;
+//# sourceMappingURL=render.d.ts.map

package/dist/core/notes/render.d.ts.map

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

@@ -0,0 +1,13 @@
+import { stringify as stringifyYaml } from 'yaml';
+/**
+ * The inverse of parseNoteText (core/notes/parse.ts): re-serializes a note
+ * back to raw file text. `undefined` frontmatter renders as no frontmatter
+ * block at all, matching parseNoteText's own treatment of absence.
+ */
+export function renderNoteText(frontmatter, body) {
+    if (!frontmatter || Object.keys(frontmatter).length === 0) {
+        return body;
+    }
+    return `---\n${stringifyYaml(frontmatter, { indent: 2 })}---\n${body}`;
+}
+//# sourceMappingURL=render.js.map

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

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

@@ -0,0 +1,26 @@
+import type { StoreConfig } from '../../config/schema.js';
+import type { Note } from './list.js';
+/**
+ * context-visibility spec: resolution order is explicit → directory default
+ * → the configured fail-closed default, and every resolution reports WHICH
+ * rung produced it — not just the resolved value — so a note relying on the
+ * fail-closed default is distinguishable from one genuinely classified.
+ */
+export type VisibilityReason = 'explicit' | 'directory default' | 'fail-closed default';
+export interface VisibilityResolution {
+    value: string;
+    reason: VisibilityReason;
+}
+export declare function resolveVisibility(config: StoreConfig, note: Note): VisibilityResolution;
+/**
+ * context-visibility spec (visibility-contexts-and-wall-verdicts): the set
+ * of visibility VALUES a requesting context can see — the one shared
+ * primitive every filtered consumer (graph pre-filter, disclosure rung 3)
+ * calls instead of raw equality. Identity default: an unconfigured context
+ * sees exactly its own value, so unconfigured stores behave exactly as
+ * before the mapping existed, and unknown contexts fail closed to it.
+ */
+export declare function visibleValuesFor(config: StoreConfig, context: string): readonly string[];
+/** Whether `context` can see a note whose resolved visibility is `value`. */
+export declare function canSee(config: StoreConfig, context: string, value: string): boolean;
+//# sourceMappingURL=visibility.d.ts.map

package/dist/core/notes/visibility.d.ts.map

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

@@ -0,0 +1,41 @@
+export function resolveVisibility(config, note) {
+    const fieldKey = config.fields.visibility;
+    const explicit = note.frontmatter?.[fieldKey];
+    if (typeof explicit === 'string' && explicit.length > 0) {
+        return { value: explicit, reason: 'explicit' };
+    }
+    const directoryDefault = findDirectoryDefault(config, note.path);
+    if (directoryDefault !== undefined) {
+        return { value: directoryDefault, reason: 'directory default' };
+    }
+    return { value: config.visibility.default_context, reason: 'fail-closed default' };
+}
+/**
+ * context-visibility spec (visibility-contexts-and-wall-verdicts): the set
+ * of visibility VALUES a requesting context can see — the one shared
+ * primitive every filtered consumer (graph pre-filter, disclosure rung 3)
+ * calls instead of raw equality. Identity default: an unconfigured context
+ * sees exactly its own value, so unconfigured stores behave exactly as
+ * before the mapping existed, and unknown contexts fail closed to it.
+ */
+export function visibleValuesFor(config, context) {
+    return config.visibility.contexts[context] ?? [context];
+}
+/** Whether `context` can see a note whose resolved visibility is `value`. */
+export function canSee(config, context, value) {
+    return visibleValuesFor(config, context).includes(value);
+}
+/** Longest matching path-prefix wins, so a more specific directory default overrides a broader one. */
+function findDirectoryDefault(config, notePath) {
+    let best;
+    for (const [prefix, value] of Object.entries(config.visibility.directory_defaults)) {
+        const normalizedPrefix = prefix.endsWith('/') ? prefix : `${prefix}/`;
+        if (notePath === prefix || notePath.startsWith(normalizedPrefix)) {
+            if (!best || prefix.length > best.prefix.length) {
+                best = { prefix, value };
+            }
+        }
+    }
+    return best?.value;
+}
+//# sourceMappingURL=visibility.js.map

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

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

@@ -0,0 +1,44 @@
+import type { StoreConfig } from '../config/schema.js';
+import { type ScannedDoc } from './conventions.js';
+/**
+ * harness-portability spec (task 8.6, revised by entry-doc-generation D5):
+ * reusable store procedures ship as contexture-OWNED skills. 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`, 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 path from AGENTS.md. Operator-authored skills live alongside,
+ * untouched by sync. Each seed names the real CLI commands built in
+ * earlier phases, in the order a judgment-driven operation uses them.
+ */
+export interface Procedure {
+    /** Skill directory slug under config.harness.procedures_path (file is `<slug>/SKILL.md`). */
+    file: string;
+    /** The human title (the H1 in the skill body). */
+    name: string;
+    /** One line for skill-discovery metadata and the AGENTS.md index. */
+    description: string;
+    content: string;
+}
+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 const PROCEDURES: readonly Procedure[];
+/**
+ * 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
+ * the canonical content syncShippedSkills writes.
+ */
+export declare function scanProcedures(root: string, config: StoreConfig): Promise<ScannedDoc[]>;
+export declare function procedurePaths(config: StoreConfig): string[];
+/**
+ * Brings every contexture-owned skill copy to the installed package's
+ * content: written when missing, rewritten when different (byte-stable —
+ * an up-to-date copy is not touched). Managed copies the installed version
+ * no longer ships (recognised by the managed header) are removed, so a
+ * renamed slug never leaves an orphan behind. Only files bearing the header
+ * are ever removed; operator skills are untouched. Returns every path it
+ * wrote or removed.
+ */
+export declare function syncShippedSkills(root: string, config: StoreConfig): Promise<string[]>;
+//# sourceMappingURL=procedures.d.ts.map

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

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

@@ -0,0 +1,154 @@
+import { mkdir, readdir, readFile, rm } from 'node:fs/promises';
+import path from 'node:path';
+import { scanDocsDir, SKILL_FILE_NAME } from './conventions.js';
+import { writeFileAtomic } from './fs/atomic.js';
+export const MANAGED_SKILL_HEADER = '<!-- Owned by contexture — written by `ctxr init`, refreshed by `ctxr update`. Do not edit; add your own skills alongside. -->';
+export const PROCEDURES = [
+    {
+        file: 'ctxr-ingest-orchestration',
+        name: 'Ingest orchestration',
+        description: 'Capture raw material into the inbox, run the dedupe check, and ingest it with source identity via the contexture CLI.',
+        content: `---
+name: ctxr-ingest-orchestration
+description: Capture raw material into the inbox, run the dedupe check, and ingest it with source identity via the contexture CLI.
+---
+
+${MANAGED_SKILL_HEADER}
+
+# Ingest orchestration
+
+1. Capture: write a plain markdown file directly into the inbox (see AGENTS.md's capture section) — no source-identity frontmatter.
+2. Check: run \`ctxr source check <path> --source-id <id>\` and read the verdict — \`new\`, \`already_ingested\`, \`alternate_source_match\`, or \`multiple_matches\`.
+3. On \`multiple_matches\`, stop and resolve the ambiguity yourself; do not guess which existing note it is.
+4. On \`new\` (or a deliberate decision to ingest anyway despite an \`alternate_source_match\`), run \`ctxr ingest <path> --source-type <type> --source-id <id>\`.
+5. The result already has a catalog entry — no separate catalog step is needed.
+`,
+    },
+    {
+        file: 'ctxr-placement',
+        name: 'Placement',
+        description: 'Choose the right taxonomy layer for a new or relocated note in this contexture store.',
+        content: `---
+name: ctxr-placement
+description: Choose the right taxonomy layer for a new or relocated note in this contexture store.
+---
+
+${MANAGED_SKILL_HEADER}
+
+# Placement
+
+1. Read AGENTS.md's "Placing a new note" section for this store's configured taxonomy layers (or lack thereof).
+2. Choose the layer whose description best matches the note; if none fits, use the catch-all location.
+3. To relocate a note that already exists (not a first placement), use \`ctxr archive <path>\` if it is being retired, or a plain tracked \`git mv\` for an ordinary re-placement — either way, the note's frontmatter (including its visibility field) is left untouched.
+4. Run \`ctxr lint\` afterward; "uningested inbox material" and "no catalog entry" findings will surface anything left unplaced.
+`,
+    },
+    {
+        file: 'ctxr-connection-finding',
+        name: 'Connection finding',
+        description: 'Find related notes via the wikilink graph of the store (neighbors, paths, hubs) and write rollups from gathered sources.',
+        content: `---
+name: ctxr-connection-finding
+description: Find related notes via the wikilink graph of the store (neighbors, paths, hubs) and write rollups from gathered sources.
+---
+
+${MANAGED_SKILL_HEADER}
+
+# Connection finding
+
+1. Run \`ctxr graph build\` to refresh the wikilink graph from the store's current notes.
+2. To find what a note connects to or from, run \`ctxr graph query neighbors <path>\` (add \`--depth\` for further hops, \`--direction in|out|both\`).
+3. To find a path between two notes, run \`ctxr graph query path <from> <to>\`.
+4. To find the most-referenced notes, run \`ctxr graph query hubs\`.
+5. Before writing a rollup for an entity, run \`ctxr rollup gather <entity>\` to enumerate candidate source notes — read those, then commit your synthesis with \`ctxr rollup write <entity> --content-file <path>\`.
+`,
+    },
+    {
+        file: 'ctxr-organize-audit',
+        name: 'Organize audit',
+        description: 'Audit store health with ctxr lint (observations) and ctxr doctor (blocking invariants).',
+        content: `---
+name: ctxr-organize-audit
+description: Audit store health with ctxr lint (observations) and ctxr doctor (blocking invariants).
+---
+
+${MANAGED_SKILL_HEADER}
+
+# Organize audit
+
+1. Run \`ctxr lint\` for a full health report — orphan notes, broken links, uningested inbox material, and catalog gaps. It always exits 0; read its findings, it never blocks anything.
+2. Run \`ctxr doctor\` to check the invariants that DO block: catalog coverage, fail-closed visibility, hook health, and more.
+3. Address doctor's failures before submitting a session; lint's findings are a judgment call for whoever is doing the audit.
+`,
+    },
+];
+/**
+ * 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
+ * the canonical content syncShippedSkills writes.
+ */
+export function scanProcedures(root, config) {
+    return scanDocsDir(root, config.harness.procedures_path);
+}
+export function procedurePaths(config) {
+    return PROCEDURES.map((p) => path.join(config.harness.procedures_path, p.file, SKILL_FILE_NAME).split(path.sep).join('/'));
+}
+/**
+ * Brings every contexture-owned skill copy to the installed package's
+ * content: written when missing, rewritten when different (byte-stable —
+ * an up-to-date copy is not touched). Managed copies the installed version
+ * no longer ships (recognised by the managed header) are removed, so a
+ * renamed slug never leaves an orphan behind. Only files bearing the header
+ * are ever removed; operator skills are untouched. Returns every path it
+ * wrote or removed.
+ */
+export async function syncShippedSkills(root, config) {
+    const changed = [];
+    for (const procedure of PROCEDURES) {
+        const relativePath = path
+            .join(config.harness.procedures_path, procedure.file, SKILL_FILE_NAME)
+            .split(path.sep)
+            .join('/');
+        const absolutePath = path.join(root, relativePath);
+        let existing;
+        try {
+            existing = await readFile(absolutePath, 'utf8');
+        }
+        catch {
+            existing = undefined;
+        }
+        if (existing !== procedure.content) {
+            await mkdir(path.dirname(absolutePath), { recursive: true });
+            await writeFileAtomic(absolutePath, procedure.content);
+            changed.push(relativePath);
+        }
+    }
+    const shippedSlugs = new Set(PROCEDURES.map((p) => p.file));
+    const skillsDir = path.join(root, config.harness.procedures_path);
+    let entries = [];
+    try {
+        entries = await readdir(skillsDir, { withFileTypes: true });
+    }
+    catch {
+        entries = [];
+    }
+    for (const entry of entries) {
+        if (!entry.isDirectory() || shippedSlugs.has(entry.name))
+            continue;
+        const skillFile = path.join(skillsDir, entry.name, SKILL_FILE_NAME);
+        let content;
+        try {
+            content = await readFile(skillFile, 'utf8');
+        }
+        catch {
+            continue;
+        }
+        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('/'));
+    }
+    return changed;
+}
+//# sourceMappingURL=procedures.js.map

package/dist/core/procedures.js.map

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

@@ -0,0 +1,16 @@
+export declare function queueAppend(storeRoot: string, targetRelativePath: string, content: string): Promise<string>;
+export interface AppliedEntry {
+    file: string;
+    target: string;
+}
+export interface ReconcileSummary {
+    applied: AppliedEntry[];
+}
+/**
+ * Applies every pending queue file to its target, oldest first, deleting
+ * each as it's applied. A malformed entry (missing header, path escaping
+ * the store, or a non-.md target) throws rather than being silently
+ * skipped or guessed at.
+ */
+export declare function reconcileQueue(storeRoot: string): Promise<ReconcileSummary>;
+//# sourceMappingURL=queue.d.ts.map

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

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