ctxr-cli 0.7.0 → 0.9.0

package/dist/config/schema.js

@@ -1,5 +1,6 @@
 import { z } from 'zod';
-import { DEFAULT_ARCHIVE_DESTINATION, DEFAULT_PUBLISH_PATH, DEFAULT_VENDORED_SKILLS } from './defaults.js';
+import { isStrictlyUnderPrefix } from '../core/fs/prefix.js';
+import { SHIPPED_DEFAULTS } from './defaults.js';
 /**
  * store-lifecycle spec: schema_version versions STORE STATE (config shape +
  * note frontmatter conventions) — a monotonic integer independent of the npm
@@ -36,7 +37,24 @@ import { DEFAULT_ARCHIVE_DESTINATION, DEFAULT_PUBLISH_PATH, DEFAULT_VENDORED_SKI
  * keys until `ctxr migrate` drops them, exactly as `identity` did when
  * remove-agent-identity retired it.
  */
-export const SUPPORTED_SCHEMA_VERSION = 8;
+/**
+ * Bumped to 9 by the capture-tier change (retain-captures-as-provenance,
+ * retain-captures-as-provenance): `ingest.capture_root` is added and
+ * `ingest.inbox_path`'s shipped default moves inside it. IngestSchema accepts
+ * a config with no `capture_root` so an unmigrated store still loads —
+ * `ctxr migrate` has to be able to read the file it is about to rewrite —
+ * and skips the nesting rule for exactly that case.
+ */
+export const SUPPORTED_SCHEMA_VERSION = 10;
+/** The version at which the capture tier became part of the store's shape, and its nesting rule enforceable. */
+export const CAPTURE_TIER_SCHEMA_VERSION = 9;
+/**
+ * Bumped to 10 by config-defaults-as-the-convention: every convention key now
+ * carries its shipped default here, and a written config omits what it agrees
+ * with. Nothing about the shape got stricter — the bump exists so the pruning
+ * migration has a `schema_version <` predicate to decide it still has work,
+ * the same way every migration in this repo does.
+ */
 export const TaxonomyLayerSchema = z.object({
     name: z.string().min(1),
     path: z.string().min(1),
@@ -48,7 +66,7 @@ const TaxonomySchema = z.object({
     layers: z.array(TaxonomyLayerSchema),
 });
 const DerivedSchema = z.object({
-    paths: z.array(z.string()),
+    paths: z.array(z.string()).default([...SHIPPED_DEFAULTS.derived.paths]),
 });
 /**
  * graph-context-document spec: the graph document's knobs. Clusters are
@@ -58,16 +76,30 @@ const DerivedSchema = z.object({
  * orphan lint check.
  */
 const GraphSettingsSchema = z.object({
-    cluster_depth: z.number().int().positive().default(2),
-    hub_top: z.number().int().positive().default(8),
-    bridge_top: z.number().int().positive().default(10),
-    orphan_exempt_clusters: z.array(z.string()).default([]),
+    cluster_depth: z.number().int().positive().default(SHIPPED_DEFAULTS.retrieval.graph.cluster_depth),
+    hub_top: z.number().int().positive().default(SHIPPED_DEFAULTS.retrieval.graph.hub_top),
+    bridge_top: z.number().int().positive().default(SHIPPED_DEFAULTS.retrieval.graph.bridge_top),
+    orphan_exempt_clusters: z.array(z.string()).default([...SHIPPED_DEFAULTS.retrieval.graph.orphan_exempt_clusters]),
 });
 const RetrievalSchema = z.object({
-    exclude_paths: z.array(z.string()),
+    exclude_paths: z.array(z.string()).default([...SHIPPED_DEFAULTS.retrieval.exclude_paths]),
+    /**
+     * compose-the-retrieval-pass spec: prefixes that remain fully retrievable —
+     * present in the catalog, present in the graph, returned by every leg — but
+     * ordered after everything else. Distinct from `exclude_paths`, which removes
+     * a path from retrieval entirely; declaring one path both ways fails doctor
+     * rather than being resolved by precedence.
+     *
+     * The shipped default demotes nothing. `init` seeds it from the resolved
+     * taxonomy's archive destination instead, which is why that seeded value is
+     * written out rather than omitted (config-defaults-as-the-convention D2).
+     */
+    demote_paths: z.array(z.string()).default([...SHIPPED_DEFAULTS.retrieval.demote_paths]),
+    /** compose-the-retrieval-pass spec: the pass's note cap; truncation is reported, never silent. */
+    gather_max_notes: z.number().int().positive().default(SHIPPED_DEFAULTS.retrieval.gather_max_notes),
     /** graph-context-document spec: relation names whose section headings type the wikilinks under them; empty = no typed edges. */
-    relations: z.array(z.string().min(1)).default([]),
-    graph: GraphSettingsSchema.default({ cluster_depth: 2, hub_top: 8, bridge_top: 10, orphan_exempt_clusters: [] }),
+    relations: z.array(z.string().min(1)).default([...SHIPPED_DEFAULTS.retrieval.relations]),
+    graph: GraphSettingsSchema.default({ ...SHIPPED_DEFAULTS.retrieval.graph, orphan_exempt_clusters: [] }),
 });
 /**
  * Recorded once, at init, from whatever branch `git init` actually created
@@ -79,17 +111,17 @@ const GitSchema = z.object({
     default_branch: z.string().min(1),
 });
 const SessionSchema = z.object({
-    branch_prefix: z.string().min(1),
-    worktrees_path: z.string().min(1),
+    branch_prefix: z.string().min(1).default(SHIPPED_DEFAULTS.session.branch_prefix),
+    worktrees_path: z.string().min(1).default(SHIPPED_DEFAULTS.session.worktrees_path),
 });
 /** session-capture-command spec (D5): declaring any path here turns the sanctioned-location gate on; empty (the default) leaves every in-store path accepted. */
 const WriteLifecycleSchema = z.object({
-    diff_size_ceiling_lines: z.number().int().positive(),
-    writable_paths: z.array(z.string()).default([]),
+    diff_size_ceiling_lines: z.number().int().positive().default(SHIPPED_DEFAULTS.write_lifecycle.diff_size_ceiling_lines),
+    writable_paths: z.array(z.string()).default([...SHIPPED_DEFAULTS.write_lifecycle.writable_paths]),
 });
 const CatalogSchema = z.object({
-    path: z.string().min(1),
-    section_max_bytes: z.number().int().positive(),
+    path: z.string().min(1).default(SHIPPED_DEFAULTS.catalog.path),
+    section_max_bytes: z.number().int().positive().default(SHIPPED_DEFAULTS.catalog.section_max_bytes),
 });
 /**
  * publish spec (design.md): unlike every other tool-owned path field, this one is
@@ -99,7 +131,7 @@ const CatalogSchema = z.object({
  * store. `init` still writes it explicitly for a freshly generated config.
  */
 const PublishSchema = z.object({
-    path: z.string().min(1).default(DEFAULT_PUBLISH_PATH),
+    path: z.string().min(1).default(SHIPPED_DEFAULTS.publish.path),
 });
 /**
  * harness-portability spec (vendored-craft-skills): which vendored
@@ -108,15 +140,24 @@ const PublishSchema = z.object({
  * out entirely — same schema-optional-with-default shape as `publish`.
  */
 const SkillsSchema = z.object({
-    vendored: z.array(z.string()).default([...DEFAULT_VENDORED_SKILLS]),
+    vendored: z.array(z.string()).default([...SHIPPED_DEFAULTS.skills.vendored]),
 });
-/** context-ingest spec: where capture lands raw material before ingest stamps identity onto it. */
-const IngestSchema = z.object({
-    inbox_path: z.string().min(1),
+/**
+ * context-ingest spec: the capture tier. `capture_root` is the retained
+ * ledger's root and `inbox_path` is the not-yet-ingested state inside it.
+ *
+ * Both paths carry the shipped convention as a schema default, so a config
+ * written before schema 9 still parses — `ctxr migrate` has to be able to
+ * read the file it is about to rewrite. The rule that the inbox sits inside
+ * the capture root lives on StoreConfigSchema instead of here, since it is a
+ * schema-9 invariant and only that scope can see the version.
+ */
+const IngestSchema = z
+    .object({
+    inbox_path: z.string().min(1).default(SHIPPED_DEFAULTS.ingest.inbox_path),
+    capture_root: z.string().min(1).default(SHIPPED_DEFAULTS.ingest.capture_root),
     /** store-primitives-from-migration-audit spec (D2): query parameters stripped when canonicalizing a URL source identity, in addition to the shipped defaults. */
-    tracking_params: z
-        .array(z.string())
-        .default(['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content', 'fbclid', 'gclid']),
+    tracking_params: z.array(z.string()).default([...SHIPPED_DEFAULTS.ingest.tracking_params]),
 });
 /**
  * context-organize spec: archive's destination — independent of taxonomy
@@ -139,7 +180,7 @@ const OrganizeSchema = z
     archive_destination: z.string().min(1).optional(),
     archive_path: z.string().min(1).optional(),
     /** store-primitives-from-migration-audit spec (D4): the grace period, in days, before a stale rollup is reported — bounds noise from a backlink edited moments ago. */
-    rollup_stale_days: z.number().int().nonnegative().default(7),
+    rollup_stale_days: z.number().int().nonnegative().default(SHIPPED_DEFAULTS.organize.rollup_stale_days),
     /**
      * context-organize spec: the store's standing current-state document
      * (priorities, active builds, back burner, sunset candidates, debt).
@@ -150,15 +191,39 @@ const OrganizeSchema = z
      */
     mission_path: z.string().min(1).optional(),
 })
-    .transform((value) => ({
-    archive_destination: value.archive_destination ?? value.archive_path ?? DEFAULT_ARCHIVE_DESTINATION,
-    rollup_stale_days: value.rollup_stale_days,
-    // Spread, not a plain key, so the output type keeps `mission_path`
-    // genuinely optional (`key?: string`) rather than always-present-but-
-    // possibly-undefined — the latter would force every `StoreConfig`
-    // object literal in the codebase to add the key just to compile.
-    ...(value.mission_path !== undefined ? { mission_path: value.mission_path } : {}),
-}));
+    .transform((value, ctx) => {
+    /**
+     * config-defaults-as-the-convention (D2): derived, not conventional — a
+     * shipped profile supplies this from the taxonomy at init. A constant
+     * default here would give every PARA store `archive/` while its own
+     * taxonomy declares `archives/`, which is the defect
+     * archive-destination-from-taxonomy exists to prevent. Absent under both
+     * spellings, the key is reported rather than guessed.
+     */
+    const archiveDestination = value.archive_destination ?? value.archive_path;
+    if (archiveDestination === undefined) {
+        ctx.addIssue({
+            code: 'custom',
+            path: ['archive_destination'],
+            message: 'organize.archive_destination is missing. It is resolved from the store taxonomy at init rather than defaulted, so declare it explicitly (or run `ctxr migrate` if this store predates the key).',
+        });
+        return z.NEVER;
+    }
+    return {
+        archive_destination: archiveDestination,
+        rollup_stale_days: value.rollup_stale_days,
+        // Spread, not a plain key, so the output type keeps `mission_path`
+        // genuinely optional (`key?: string`) rather than always-present-but-
+        // possibly-undefined — the latter would force every `StoreConfig`
+        // object literal in the codebase to add the key just to compile.
+        //
+        // config-defaults-as-the-convention (D2): an opt-in key, deliberately
+        // NOT defaulted. Call sites branch on its presence to decide whether the
+        // store has a mission mechanism at all, so defaulting it would switch
+        // that on for every store predating it, pointing at a document none has.
+        ...(value.mission_path !== undefined ? { mission_path: value.mission_path } : {}),
+    };
+});
 /**
  * harness-portability spec: the portable skill pack and the guidance
  * documents (a shipped baseline convention file, the operator's own
@@ -193,24 +258,25 @@ const HarnessSchema = z
      * compose-store-guidance-documents design.md D6: a size ceiling on
      * AGENTS.md's inlined "Store conventions" section, guarding against
      * unbounded growth now that its content is inlined rather than indexed
-     * (inline-conventions-and-mission). Optional with no schema-level
-     * default (falls back to `DEFAULT_CONVENTION_MAX_BYTES` at the one
-     * doctor check that reads it) so this stays purely additive — no
-     * existing `StoreConfig` object literal needs updating to compile.
+     * (inline-conventions-and-mission). A convention key like any other
+     * since config-defaults-as-the-convention: the default is declared here
+     * rather than applied by the one doctor check that reads it, so the check
+     * and the schema cannot disagree about the budget.
      */
-    convention_max_bytes: z.number().int().positive().optional(),
+    convention_max_bytes: z.number().int().positive().default(SHIPPED_DEFAULTS.harness.convention_max_bytes),
 })
-    .transform((value, ctx) => {
-    const skillsPath = value.skills_path ?? value.procedures_path;
-    if (skillsPath === undefined) {
-        ctx.addIssue({
-            code: z.ZodIssueCode.custom,
-            path: ['skills_path'],
-            message: 'harness.skills_path is missing. If this store predates the skills-path rename, run `ctxr migrate`.',
-        });
-        return z.NEVER;
-    }
-    const guidancePath = value.guidance_path ?? value.conventions_path ?? '.contexture/guidance/';
+    .transform((value) => {
+    /**
+     * config-defaults-as-the-convention: the pre-rename spellings are still
+     * read first, so an unmigrated store keeps the path it declared. What
+     * changed is the end of the chain — absent under BOTH spellings used to
+     * raise a custom "run `ctxr migrate`" error, but an unmigrated store HAS
+     * `procedures_path` and never reached it. What it actually rejected was a
+     * config declining to name a skills path, which is now a config that
+     * accepts the shipped one.
+     */
+    const skillsPath = value.skills_path ?? value.procedures_path ?? SHIPPED_DEFAULTS.harness.skills_path;
+    const guidancePath = value.guidance_path ?? value.conventions_path ?? SHIPPED_DEFAULTS.harness.guidance_path;
     // Spread, not a plain key, so the output type keeps `convention_max_bytes`
     // genuinely optional (`key?: number`) rather than always-present-but-possibly-undefined
     // (`key: number | undefined`) — the latter would require every existing
@@ -218,7 +284,7 @@ const HarnessSchema = z
     return {
         skills_path: skillsPath,
         guidance_path: guidancePath,
-        ...(value.convention_max_bytes !== undefined ? { convention_max_bytes: value.convention_max_bytes } : {}),
+        convention_max_bytes: value.convention_max_bytes,
     };
 });
 /**
@@ -253,18 +319,41 @@ export const StoreConfigSchema = z
     .object({
     schema_version: z.number().int().positive(),
     taxonomy: TaxonomySchema,
-    derived: DerivedSchema,
-    retrieval: RetrievalSchema,
+    // `prefault`, not `default`: it substitutes an INPUT, so the block's own
+    // per-key defaults fill it in. `.default({})` would demand a fully
+    // resolved output object here and duplicate every value a second time.
+    derived: DerivedSchema.prefault({}),
+    retrieval: RetrievalSchema.prefault({}),
     git: GitSchema,
-    session: SessionSchema,
-    write_lifecycle: WriteLifecycleSchema,
-    catalog: CatalogSchema,
-    publish: PublishSchema.default({ path: DEFAULT_PUBLISH_PATH }),
-    skills: SkillsSchema.default({ vendored: [...DEFAULT_VENDORED_SKILLS] }),
-    ingest: IngestSchema,
+    session: SessionSchema.prefault({}),
+    write_lifecycle: WriteLifecycleSchema.prefault({}),
+    catalog: CatalogSchema.prefault({}),
+    publish: PublishSchema.prefault({}),
+    skills: SkillsSchema.prefault({}),
+    ingest: IngestSchema.prefault({}),
     organize: OrganizeSchema,
-    harness: HarnessSchema,
-    adapters: AdaptersFieldSchema,
+    harness: HarnessSchema.prefault({}),
+    adapters: AdaptersFieldSchema.default([...SHIPPED_DEFAULTS.adapters]),
 })
-    .passthrough();
+    .passthrough()
+    .superRefine((value, ctx) => {
+    /**
+     * retain-captures-as-provenance (D7): one prefix has to serve both the
+     * retrieval exclusion and the write-path gate, which only holds while the
+     * inbox is strictly inside the capture root. Gated on the version that
+     * introduced the capture tier — a store still on an older schema has a
+     * `capture_root` this schema defaulted in, not one it declared, and
+     * migrations of earlier versions must be able to write their configs
+     * back untouched.
+     */
+    if (value.schema_version < CAPTURE_TIER_SCHEMA_VERSION)
+        return;
+    if (!isStrictlyUnderPrefix(value.ingest.inbox_path, value.ingest.capture_root)) {
+        ctx.addIssue({
+            code: 'custom',
+            path: ['ingest', 'inbox_path'],
+            message: `"${value.ingest.inbox_path}" must be a directory inside capture_root ("${value.ingest.capture_root}")`,
+        });
+    }
+});
 //# sourceMappingURL=schema.js.map

package/dist/config/schema.js.map

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

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package/dist/core/agents-doc.js

@@ -78,7 +78,10 @@ export async function buildAgentsLegRoutingSection(root, config) {
  */
 export const AGENTS_MD_CAPTURE_FENCE = htmlCommentFence('capture-and-ingest');
 export function renderCaptureSection(config) {
-    return agentsTemplate('capture-and-ingest').replaceAll('__INBOX_PATH__', config.ingest.inbox_path).split('\n');
+    return agentsTemplate('capture-and-ingest')
+        .replaceAll('__INBOX_PATH__', config.ingest.inbox_path)
+        .replaceAll('__CAPTURE_ROOT__', config.ingest.capture_root)
+        .split('\n');
 }
 export async function buildAgentsCaptureSection(root, config) {
     return upsertFencedRegionInFile(agentsMdPath(root), AGENTS_MD_CAPTURE_FENCE, renderCaptureSection(config));

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

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

@@ -4,7 +4,7 @@
  * (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
+ * the schema's shipped default) fails doctor loud rather than silently
  * truncating content the inlining exists to surface.
  */
 export declare const conventionsSectionSizeCheck: import("./types.js").CheckDefinition;

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

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

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

@@ -1,4 +1,3 @@
-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';
@@ -8,7 +7,7 @@ import { defineCheck } from './types.js';
  * (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
+ * the schema's shipped default) fails doctor loud rather than silently
  * truncating content the inlining exists to surface.
  */
 export const conventionsSectionSizeCheck = defineCheck({
@@ -23,7 +22,7 @@ export const conventionsSectionSizeCheck = defineCheck({
             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;
+        const budget = ctx.config.harness.convention_max_bytes;
         if (size <= budget)
             return { status: 'pass', findings: [] };
         const finding = {

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

@@ -1 +1 @@
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+{"version":3,"file":"harness-portability-checks.js","sourceRoot":"","sources":["../../../src/core/checks/harness-portability-checks.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,2BAA2B,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAE7E,OAAO,EAAE,wBAAwB,EAAE,MAAM,wBAAwB,CAAC;AAClE,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAEzC;;;;;;;;GAQG;AACH,MAAM,CAAC,MAAM,2BAA2B,GAAG,WAAW,CAAC;IACrD,EAAE,EAAE,8CAA8C;IAClD,KAAK,EAAE,2FAA2F;IAClG,QAAQ,EAAE,WAAW;IACrB,UAAU,EAAE,qBAAqB;IACjC,MAAM,EAAE,CAAC,OAAO,CAAC;IACjB,KAAK,CAAC,GAAG,CAAC,GAAG;QACX,MAAM,MAAM,GAAG,MAAM,wBAAwB,CAAC,YAAY,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,2BAA2B,CAAC,CAAC;QACxG,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACxB,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,0DAA0D,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC;QAClH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC,CAAC;QAC1D,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,oBAAoB,CAAC;QACvD,IAAI,IAAI,IAAI,MAAM;YAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC;QAE5D,MAAM,OAAO,GAAY;YACvB,IAAI,EAAE,uDAAuD;YAC7D,QAAQ,EAAE,OAAO;YACjB,OAAO,EAAE,8CAA8C,IAAI,8CAA8C,MAAM,+EAA+E;YAC9L,OAAO,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;SAC1B,CAAC;QACF,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC;IACjD,CAAC;CACF,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,0BAA0B,GAAG,CAAC,2BAA2B,CAAC,CAAC"}

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":"AAKA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAElD;;;GAGG;AACH,eAAO,MAAM,MAAM,EAAE,SAAS,eAAe,EAM5C,CAAC"}
+{"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,EAO5C,CAAC"}

package/dist/core/checks/manifest.js

@@ -2,6 +2,7 @@ import { CATALOG_CHECKS } from './catalog-checks.js';
 import { HARNESS_PORTABILITY_CHECKS } from './harness-portability-checks.js';
 import { INTEGRITY_CHECKS } from './integrity-checks.js';
 import { ORGANIZE_CHECKS } from './organize-checks.js';
+import { RETRIEVAL_CHECKS } from './retrieval-checks.js';
 import { WRITE_LIFECYCLE_CHECKS } from './write-lifecycle-checks.js';
 /**
  * The only file later phases append to when they add a doctor/lint check:
@@ -11,6 +12,7 @@ export const CHECKS = [
     ...WRITE_LIFECYCLE_CHECKS,
     ...CATALOG_CHECKS,
     ...ORGANIZE_CHECKS,
+    ...RETRIEVAL_CHECKS,
     ...INTEGRITY_CHECKS,
     ...HARNESS_PORTABILITY_CHECKS,
 ];

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,0BAA0B,EAAE,MAAM,iCAAiC,CAAC;AAC7E,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,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,GAAG,sBAAsB;IACzB,GAAG,cAAc;IACjB,GAAG,eAAe;IAClB,GAAG,gBAAgB;IACnB,GAAG,0BAA0B;CAC9B,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,0BAA0B,EAAE,MAAM,iCAAiC,CAAC;AAC7E,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AACvD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAC;AAGrE;;;GAGG;AACH,MAAM,CAAC,MAAM,MAAM,GAA+B;IAChD,GAAG,sBAAsB;IACzB,GAAG,cAAc;IACjB,GAAG,eAAe;IAClB,GAAG,gBAAgB;IACnB,GAAG,gBAAgB;IACnB,GAAG,0BAA0B;CAC9B,CAAC"}

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

@@ -10,7 +10,17 @@ export declare const orphanNotesCheck: import("./types.js").CheckDefinition;
  * `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. */
+/**
+ * context-organize: material still sitting in the inbox.
+ *
+ * Read off the filesystem, not out of `ctx.notes()`. The inbox lives inside
+ * the capture tier, which is a declared retrieval exclusion, so a capture is
+ * not a note and note enumeration cannot see it — a version of this check
+ * that filtered notes would report nothing, forever, and look healthy doing
+ * it. Location is also the whole condition: a capture pipeline may write a
+ * source type and id at capture time, so absent frontmatter no longer
+ * distinguishes ingested from not. Leaving the inbox is what ingest does.
+ */
 export declare const uningestedInboxCheck: import("./types.js").CheckDefinition;
 /**
  * context-organize spec: "notes with no catalog entry as covered by

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

@@ -1 +1 @@
-{"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;;;;;;;GAOG;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"}
+{"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;;;;;;;;;;GAUG;AACH,eAAO,MAAM,oBAAoB,sCAmB/B,CAAC;AAsBH;;;;;;;GAOG;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"}

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

@@ -1,9 +1,9 @@
-import { readFile } from 'node:fs/promises';
+import { readdir, readFile } from 'node:fs/promises';
+import path from 'node:path';
 import { AGENTS_MD_SECTION_ORDER, agentsMdPath } from '../agents-doc.js';
 import { checkCatalogCoverage } from '../catalog/build.js';
 import { reorderFencedRegions } from '../fs/fenced-region.js';
 import { orphans } from '../graph/query.js';
-import { hasSourceIdentity } from '../ingest/identity.js';
 import { findStaleRollups } from '../rollup.js';
 import { defineCheck } from './types.js';
 const GRAPH_SKIP_REASON = 'graph has not been built yet — run `ctxr graph build`';
@@ -58,7 +58,17 @@ export const brokenLinksCheck = defineCheck({
         return { status: findings.length > 0 ? 'fail' : 'pass', findings };
     },
 });
-/** context-ingest / context-organize: material captured but never stamped with source identity. */
+/**
+ * context-organize: material still sitting in the inbox.
+ *
+ * Read off the filesystem, not out of `ctx.notes()`. The inbox lives inside
+ * the capture tier, which is a declared retrieval exclusion, so a capture is
+ * not a note and note enumeration cannot see it — a version of this check
+ * that filtered notes would report nothing, forever, and look healthy doing
+ * it. Location is also the whole condition: a capture pipeline may write a
+ * source type and id at capture time, so absent frontmatter no longer
+ * distinguishes ingested from not. Leaving the inbox is what ingest does.
+ */
 export const uningestedInboxCheck = defineCheck({
     id: 'organize.uningested_inbox_material',
     title: 'Inbox material not yet ingested',
@@ -66,21 +76,41 @@ export const uningestedInboxCheck = defineCheck({
     capability: 'context-organize',
     scopes: ['store'],
     async run(ctx) {
-        const notes = await ctx.notes();
-        const prefix = ctx.config.ingest.inbox_path.endsWith('/')
-            ? ctx.config.ingest.inbox_path
-            : `${ctx.config.ingest.inbox_path}/`;
-        const findings = notes
-            .filter((note) => note.path.startsWith(prefix) && !hasSourceIdentity(note))
-            .map((note) => ({
+        const inboxPath = ctx.config.ingest.inbox_path;
+        const findings = (await filesUnder(path.join(ctx.storeRoot, inboxPath)))
+            .map((relativeToInbox) => `${inboxPath.replace(/\/+$/, '')}/${relativeToInbox}`)
+            .sort()
+            .map((capturePath) => ({
             code: 'organize.uningested_inbox_material',
             severity: 'info',
-            message: `"${note.path}" is in the inbox but has not been ingested.`,
-            subject: note.path,
+            message: `"${capturePath}" is in the inbox but has not been ingested.`,
+            subject: capturePath,
         }));
         return { status: findings.length > 0 ? 'fail' : 'pass', findings };
     },
 });
+/** Every file under `dir`, recursively, as forward-slash paths relative to it. An absent directory has none. */
+async function filesUnder(dir) {
+    let entries;
+    try {
+        entries = await readdir(dir, { withFileTypes: true });
+    }
+    catch (err) {
+        if (err.code === 'ENOENT')
+            return [];
+        throw err;
+    }
+    const found = [];
+    for (const entry of entries) {
+        if (entry.isDirectory()) {
+            found.push(...(await filesUnder(path.join(dir, entry.name))).map((nested) => `${entry.name}/${nested}`));
+        }
+        else if (entry.isFile() && entry.name !== '.gitkeep') {
+            found.push(entry.name);
+        }
+    }
+    return found;
+}
 /**
  * context-organize spec: "notes with no catalog entry as covered by
  * context-catalog" — the same underlying condition as `catalogCoverageCheck`