kibi-cli 2.18.0 → 2.20.0

package/dist/cli-operation-metadata.d.ts

@@ -23,7 +23,7 @@ export declare const CLI_OPERATION_METADATA: readonly [{
 }, {
     readonly name: "kb_query";
     readonly cliName: "query";
-    readonly description: "Read entities from the KB with filters. Use for discovery and lookup before edits. Do not use for writes. No mutation side effects. Tags filter by metadata tags only, not entity IDs.";
+    readonly description: "Read entities from the KB with exact filters, or ask typed fact questions. Use for lookup by id, type, tags or sourceFile, and for precise questions about modeled facts: predicate facts by name with named arguments (predicate + where), property facts of a subject (subjectKey + propertyKey), or the catalog of facts of one kind (factKind; 'predicate_schema' lists the predicates you can ask about with their argument names and constants). Typed answers return matching fact rows plus factQuery: the schema used, distinct counts, values that do exist when nothing matched, warnings about the question and the next call to make. Read-only. Tags filter by metadata tags only, not entity IDs.";
 }, {
     readonly name: "kb_search";
     readonly cliName: "search";
@@ -59,7 +59,7 @@ export declare const CLI_OPERATION_METADATA: readonly [{
 }, {
     readonly name: "kb_model";
     readonly cliName: "model";
-    readonly description: "Turn requirement prose into checkable structure without writing the KB. mode:analyze returns the semantic advisor receipt: the clause ledger, what is grounded, what is ambiguous and suggested modeling (pass clauses for compound prose and optional typed kibi.logic.v1 interpretations). mode:requirement converts one claim (subjectKey, propertyKey, operator, value, or typed logic) into a strict-lane write set and applyPlan. mode:predicates ranks ontology predicate schemas and returns an applicable predicate-fact plan only for reviewed bindings, otherwise an ontology-gap observation. Apply returned plans with kb_upsert.";
+    readonly description: "Turn requirement prose into checkable structure without writing the KB. mode:analyze returns the semantic advisor receipt: the clause ledger, what is grounded, what is ambiguous and suggested modeling (pass clauses for compound prose and optional typed kibi.logic.v1 interpretations). mode:requirement converts one claim (subjectKey, propertyKey, operator, value, or typed logic) into a strict-lane write set and applyPlan. mode:predicates ranks ontology predicate schemas and returns an applicable predicate-fact plan only for reviewed bindings, otherwise an ontology-gap observation. With requirementId, mode:predicates also returns a hash-bound plan (fact write plus requires_predicate link) for kb_apply_plan, whose contradictionAnalysis is the what-if over the current KB; other returned plans apply with kb_upsert, and kb_upsert dryRun with plannedFacts previews a requirement before its facts exist.";
 }, {
     readonly name: "kb_plan_bootstrap";
     readonly cliName: "plan-bootstrap";

package/dist/cli-operation-metadata.js

@@ -25,7 +25,7 @@ export const CLI_OPERATION_METADATA = [
     {
         name: "kb_query",
         cliName: "query",
-        description: "Read entities from the KB with filters. Use for discovery and lookup before edits. Do not use for writes. No mutation side effects. Tags filter by metadata tags only, not entity IDs.",
+        description: "Read entities from the KB with exact filters, or ask typed fact questions. Use for lookup by id, type, tags or sourceFile, and for precise questions about modeled facts: predicate facts by name with named arguments (predicate + where), property facts of a subject (subjectKey + propertyKey), or the catalog of facts of one kind (factKind; 'predicate_schema' lists the predicates you can ask about with their argument names and constants). Typed answers return matching fact rows plus factQuery: the schema used, distinct counts, values that do exist when nothing matched, warnings about the question and the next call to make. Read-only. Tags filter by metadata tags only, not entity IDs.",
     },
     {
         name: "kb_search",
@@ -70,7 +70,7 @@ export const CLI_OPERATION_METADATA = [
     {
         name: "kb_model",
         cliName: "model",
-        description: "Turn requirement prose into checkable structure without writing the KB. mode:analyze returns the semantic advisor receipt: the clause ledger, what is grounded, what is ambiguous and suggested modeling (pass clauses for compound prose and optional typed kibi.logic.v1 interpretations). mode:requirement converts one claim (subjectKey, propertyKey, operator, value, or typed logic) into a strict-lane write set and applyPlan. mode:predicates ranks ontology predicate schemas and returns an applicable predicate-fact plan only for reviewed bindings, otherwise an ontology-gap observation. Apply returned plans with kb_upsert.",
+        description: "Turn requirement prose into checkable structure without writing the KB. mode:analyze returns the semantic advisor receipt: the clause ledger, what is grounded, what is ambiguous and suggested modeling (pass clauses for compound prose and optional typed kibi.logic.v1 interpretations). mode:requirement converts one claim (subjectKey, propertyKey, operator, value, or typed logic) into a strict-lane write set and applyPlan. mode:predicates ranks ontology predicate schemas and returns an applicable predicate-fact plan only for reviewed bindings, otherwise an ontology-gap observation. With requirementId, mode:predicates also returns a hash-bound plan (fact write plus requires_predicate link) for kb_apply_plan, whose contradictionAnalysis is the what-if over the current KB; other returned plans apply with kb_upsert, and kb_upsert dryRun with plannedFacts previews a requirement before its facts exist.",
     },
     {
         name: "kb_plan_bootstrap",

package/dist/cli-register-maintenance.js

@@ -14,7 +14,7 @@ export function registerMaintenanceCommands(program) {
         .action(async () => (await import("./commands/engine.js")).engineStopCommand());
     engine
         .command("janitor")
-        .description("Classify and clean stale engine daemons and branch-store locks (crashed engines, removed worktrees)")
+        .description("Classify and clean stale engine daemons, branch-store locks and expired lock-takeover records (crashed engines, removed worktrees)")
         .option("--all", "Also sweep runtime-directory daemon sockets from other workspaces", false)
         .option("--apply", "Execute cleanups (default: report only)", false)
         .option("--format <format>", "Output format: json|table", "table")

package/dist/commands/doctor.js

@@ -694,14 +694,19 @@ function checkBranchStore() {
     const compilation = branchStoreCompilation(store);
     // implements REQ-core-journaled-engine-persistence
     const takeover = storeLockTakeoverReason(store.path);
+    // A takeover is reported whether or not the store holds a compilation yet.
+    const withTakeover = (message) => takeover
+        ? `${message}${message.endsWith(".") ? "" : "."} ${String(takeover.detail)}`
+        : message;
+    const takeoverDetails = takeover ? { lockTakeover: takeover } : {};
     if (compilation.compiled) {
         return {
             passed: true,
-            message: `Compiled for ${branch}${compilation.generation ? ` (${compilation.generation})` : ""}${takeover ? `. ${String(takeover.detail)}` : ""}`,
+            message: withTakeover(`Compiled for ${branch}${compilation.generation ? ` (${compilation.generation})` : ""}`),
             details: {
                 ...details,
                 generation: compilation.generation,
-                ...(takeover ? { lockTakeover: takeover } : {}),
+                ...takeoverDetails,
             },
         };
     }
@@ -709,18 +714,19 @@ function checkBranchStore() {
     if (reason === null) {
         return {
             passed: true,
-            message: `Not compiled yet for ${branch}; .kb/ holds no authored sources`,
-            details,
+            message: withTakeover(`Not compiled yet for ${branch}; .kb/ holds no authored sources`),
+            details: { ...details, ...takeoverDetails },
         };
     }
     return {
         passed: false,
-        message: String(reason.detail),
+        message: withTakeover(String(reason.detail)),
         remediation: "Run: kibi sync",
         details: {
             ...details,
             generation: compilation.generation,
             authoredSources: reason.authoredSources,
+            ...takeoverDetails,
         },
     };
 }

package/dist/commands/engine.d.ts

@@ -9,7 +9,8 @@ export interface EngineJanitorOptions {
 /**
  * Classify and (optionally) clean stale engine daemons and branch-store
  * locks: crashed engines leave ownership journals behind, worktree removals
- * strand live daemons, dead daemons leave sockets. Report-only by default;
+ * strand live daemons, dead daemons leave sockets, and stale-lock takeover
+ * records outlive the window kb_status reports them for. Report-only by default;
  `--apply` executes the clean actions.
  */
 export declare function engineJanitorCommand(options: EngineJanitorOptions): Promise<void>;

package/dist/commands/engine.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../../src/commands/engine.ts"],"names":[],"mappings":"AAuCA,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,IAAI,CAAC,CA4BzD;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,IAAI,CAAC,CAWvD;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC,CAE1D;AAED,MAAM,WAAW,oBAAoB;IACnC,QAAQ,CAAC,GAAG,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IACzB,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;CAC1B;AAED;;;;;GAKG;AAEH,wBAAsB,oBAAoB,CACxC,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,IAAI,CAAC,CA2Cf;AAED,wBAAsB,qBAAqB,IAAI,OAAO,CAAC,IAAI,CAAC,CAkB3D;AAED,wBAAsB,oBAAoB,CAAC,OAAO,EAAE;IAClD,MAAM,EAAE,MAAM,CAAC;CAChB,GAAG,OAAO,CAAC,IAAI,CAAC,CAWhB"}
+{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../../src/commands/engine.ts"],"names":[],"mappings":"AAuCA,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,IAAI,CAAC,CA4BzD;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,IAAI,CAAC,CAWvD;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC,CAE1D;AAED,MAAM,WAAW,oBAAoB;IACnC,QAAQ,CAAC,GAAG,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IACzB,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;CAC1B;AAED;;;;;;GAMG;AAEH,wBAAsB,oBAAoB,CACxC,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAiDf;AAED,wBAAsB,qBAAqB,IAAI,OAAO,CAAC,IAAI,CAAC,CAkB3D;AAED,wBAAsB,oBAAoB,CAAC,OAAO,EAAE;IAClD,MAAM,EAAE,MAAM,CAAC;CAChB,GAAG,OAAO,CAAC,IAAI,CAAC,CAWhB"}

package/dist/commands/engine.js

@@ -74,7 +74,8 @@ export async function storageStatusCommand() {
 /**
  * Classify and (optionally) clean stale engine daemons and branch-store
  * locks: crashed engines leave ownership journals behind, worktree removals
- * strand live daemons, dead daemons leave sockets. Report-only by default;
+ * strand live daemons, dead daemons leave sockets, and stale-lock takeover
+ * records outlive the window kb_status reports them for. Report-only by default;
  `--apply` executes the clean actions.
  */
 // implements REQ-core-journaled-engine-persistence
@@ -98,6 +99,10 @@ export async function engineJanitorCommand(options) {
         return;
     }
     for (const finding of findings) {
+        if (finding.kind === "takeover-record") {
+            console.log(`[${finding.action}] takeover record ${finding.recordPath} at=${finding.at} (past the kb_status notice window)`);
+            continue;
+        }
         const holder = "pid" in finding && finding.pid !== undefined
             ? ` pid=${finding.pid}`
             : "";

package/dist/commands/sync/manifest.d.ts

@@ -33,6 +33,16 @@ export declare function refreshManifestCoordinates(manifestPath: string, workspa
     refreshSymbolCoordinates?: boolean;
     quiet?: boolean;
 }): Promise<void>;
+/**
+ * Rewrite a symbol manifest whose `symbols` sequence is in YAML flow layout
+ * (`symbols: [ { id: … }, … ]`) as block YAML, keeping comments and entry
+ * order. kibi-cli before 2.18.0 appended to the `symbols: []` that
+ * `kibi init` writes and kept every symbol on that one line; the hook
+ * scanners of older adapters cannot read it and diffs of it are unreviewable,
+ * so plain `kibi sync` normalises it once. Returns the number of symbols
+ * when the file was rewritten, otherwise null.
+ */
+export declare function normalizeManifestLayout(manifestPath: string, deps?: Partial<ManifestDeps>): number | null;
 export declare function hasAllGeneratedCoordinates(entry: ManifestSymbolEntry): boolean;
 export declare function isEligibleForCoordinateRefresh(sourceFile: string | undefined, workspaceRoot: string, deps?: Partial<ManifestDeps>): boolean;
 //# sourceMappingURL=manifest.d.ts.map

package/dist/commands/sync/manifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/manifest.ts"],"names":[],"mappings":"AAkBA,OAAO,EACL,UAAU,EACV,YAAY,EACZ,UAAU,EACV,UAAU,EACV,aAAa,EACd,MAAM,SAAS,CAAC;AAEjB,OAAO,EAAE,IAAI,IAAI,QAAQ,EAAE,IAAI,IAAI,SAAS,EAAE,MAAM,SAAS,CAAC;AAC9D,OAAO,EAML,uBAAuB,EACxB,MAAM,wCAAwC,CAAC;AAChD,OAAO,EACL,KAAK,mBAAmB,EACxB,uBAAuB,EACxB,MAAM,yCAAyC,CAAC;AACjD,OAAO,EACL,0BAA0B,EAG3B,MAAM,oCAAoC,CAAC;AAC5C,OAAO,EAAE,2BAA2B,EAAE,MAAM,+BAA+B,CAAC;AAE5E,UAAU,YAAY;IACpB,QAAQ,EAAE,OAAO,QAAQ,CAAC;IAC1B,uBAAuB,EAAE,OAAO,uBAAuB,CAAC;IACxD,UAAU,EAAE,OAAO,UAAU,CAAC;IAC9B,SAAS,EAAE,OAAO,SAAS,CAAC;IAC5B,YAAY,EAAE,OAAO,YAAY,CAAC;IAClC,UAAU,EAAE,OAAO,UAAU,CAAC;IAC9B,UAAU,EAAE,OAAO,UAAU,CAAC;IAC9B,aAAa,EAAE,OAAO,aAAa,CAAC;IACpC,uBAAuB,EAAE,OAAO,uBAAuB,CAAC;IACxD,2BAA2B,EAAE,OAAO,2BAA2B,CAAC;CACjE;AAkBD,eAAO,MAAM,8BAA8B,QAc1C,CAAC;AAaF;;;;;;;;;GASG;AACH,OAAO,EAAE,0BAA0B,EAAE,CAAC;AAEtC,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,mBAAmB,GAAG,OAAO,CAG7E;AAoHD,wBAAsB,0BAA0B,CAE9C,YAAY,EAAE,MAAM,EACpB,aAAa,EAAE,MAAM,EACrB,IAAI,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,GAAG;IAC7B,wBAAwB,CAAC,EAAE,OAAO,CAAC;IACnC,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GACA,OAAO,CAAC,IAAI,CAAC,CA0Mf;AAED,wBAAgB,0BAA0B,CAExC,KAAK,EAAE,mBAAmB,GACzB,OAAO,CAOT;AAED,wBAAgB,8BAA8B,CAE5C,UAAU,EAAE,MAAM,GAAG,SAAS,EAC9B,aAAa,EAAE,MAAM,EACrB,IAAI,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,GAC3B,OAAO,CAUT"}
+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/manifest.ts"],"names":[],"mappings":"AAkBA,OAAO,EACL,UAAU,EACV,YAAY,EACZ,UAAU,EACV,UAAU,EACV,aAAa,EACd,MAAM,SAAS,CAAC;AAEjB,OAAO,EAAE,IAAI,IAAI,QAAQ,EAAE,IAAI,IAAI,SAAS,EAAE,MAAM,SAAS,CAAC;AAE9D,OAAO,EAML,uBAAuB,EACxB,MAAM,wCAAwC,CAAC;AAChD,OAAO,EACL,KAAK,mBAAmB,EACxB,uBAAuB,EACxB,MAAM,yCAAyC,CAAC;AACjD,OAAO,EACL,0BAA0B,EAG3B,MAAM,oCAAoC,CAAC;AAC5C,OAAO,EAAE,2BAA2B,EAAE,MAAM,+BAA+B,CAAC;AAG5E,UAAU,YAAY;IACpB,QAAQ,EAAE,OAAO,QAAQ,CAAC;IAC1B,uBAAuB,EAAE,OAAO,uBAAuB,CAAC;IACxD,UAAU,EAAE,OAAO,UAAU,CAAC;IAC9B,SAAS,EAAE,OAAO,SAAS,CAAC;IAC5B,YAAY,EAAE,OAAO,YAAY,CAAC;IAClC,UAAU,EAAE,OAAO,UAAU,CAAC;IAC9B,UAAU,EAAE,OAAO,UAAU,CAAC;IAC9B,aAAa,EAAE,OAAO,aAAa,CAAC;IACpC,uBAAuB,EAAE,OAAO,uBAAuB,CAAC;IACxD,2BAA2B,EAAE,OAAO,2BAA2B,CAAC;CACjE;AAkBD,eAAO,MAAM,8BAA8B,QAc1C,CAAC;AAaF;;;;;;;;;GASG;AACH,OAAO,EAAE,0BAA0B,EAAE,CAAC;AAEtC,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,mBAAmB,GAAG,OAAO,CAG7E;AAoHD,wBAAsB,0BAA0B,CAE9C,YAAY,EAAE,MAAM,EACpB,aAAa,EAAE,MAAM,EACrB,IAAI,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,GAAG;IAC7B,wBAAwB,CAAC,EAAE,OAAO,CAAC;IACnC,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GACA,OAAO,CAAC,IAAI,CAAC,CA0Mf;AAED;;;;;;;;GAQG;AAEH,wBAAgB,uBAAuB,CACrC,YAAY,EAAE,MAAM,EACpB,IAAI,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,GAC3B,MAAM,GAAG,IAAI,CAWf;AAED,wBAAgB,0BAA0B,CAExC,KAAK,EAAE,mBAAmB,GACzB,OAAO,CAOT;AAED,wBAAgB,8BAA8B,CAE5C,UAAU,EAAE,MAAM,GAAG,SAAS,EAC9B,aAAa,EAAE,MAAM,EACrB,IAAI,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,GAC3B,OAAO,CAUT"}

package/dist/commands/sync/manifest.js

@@ -18,10 +18,12 @@
 import { existsSync, readFileSync, renameSync, unlinkSync, writeFileSync, } from "node:fs";
 import * as path from "node:path";
 import { dump as dumpYAML, load as parseYAML } from "js-yaml";
+import { isSeq, parseDocument } from "yaml";
 import { coarseCoordinateSpan, coordinateIdentityHash, coordinateSourceHash, parseCoordinateArtifact, writeCoordinateArtifact, } from "../../extractors/symbol-coordinates.js";
 import { enrichSymbolCoordinates, } from "../../extractors/symbols-coordinator.js";
 import { COARSE_GRANULARITY_REASONS, COARSE_GRANULARITY_REASONS_PARENTHESIZED, isCoarseGranularityReason, } from "../../public/symbol-granularity.js";
 import { resolveSymbolsManifestPaths } from "../../utils/manifest-paths.js";
+import { blockifySymbolManifest } from "../../utils/symbol-manifest-layout.js";
 function resolveDeps(overrides) {
     return {
         dumpYAML,
@@ -307,6 +309,31 @@ manifestPath, workspaceRoot, deps) {
         }
     }
 }
+/**
+ * Rewrite a symbol manifest whose `symbols` sequence is in YAML flow layout
+ * (`symbols: [ { id: … }, … ]`) as block YAML, keeping comments and entry
+ * order. kibi-cli before 2.18.0 appended to the `symbols: []` that
+ * `kibi init` writes and kept every symbol on that one line; the hook
+ * scanners of older adapters cannot read it and diffs of it are unreviewable,
+ * so plain `kibi sync` normalises it once. Returns the number of symbols
+ * when the file was rewritten, otherwise null.
+ */
+// implements REQ-kibi-hooks-flow-manifest
+export function normalizeManifestLayout(manifestPath, deps) {
+    const resolved = resolveDeps(deps);
+    const rawContent = String(resolved.readFileSync(manifestPath, "utf8"));
+    const doc = parseDocument(rawContent);
+    const symbols = doc.get("symbols", true);
+    if (!isSeq(symbols) || symbols.items.length === 0)
+        return null;
+    if (!blockifySymbolManifest(doc))
+        return null;
+    const nextContent = doc.toString({ lineWidth: 0 });
+    if (nextContent === rawContent)
+        return null;
+    publishAtomically(manifestPath, nextContent, resolved);
+    return symbols.items.length;
+}
 export function hasAllGeneratedCoordinates(
 // implements REQ-003
 entry) {

package/dist/commands/sync/untracked-targets.d.ts

@@ -20,5 +20,22 @@ interface UntrackedTargetsDeps {
  * the diagnostic can never break a sync run.
  */
 export declare function findUntrackedDocumentMatches(workspaceRoot: string, missingIds: readonly string[], deps?: Partial<UntrackedTargetsDeps>): Map<string, string>;
+/**
+ * Give an upsert-only symbol manifest the pending-source receipt kb_upsert
+ * writes since it learned to (`writeSourceForUpsert`).
+ *
+ * Older Kibi appended symbols to the untracked `.kb/symbols.yaml` that
+ * `kibi init` creates without a receipt. The upsert wrote those symbols into
+ * the store directly, but sync never saw the manifest, so the store recorded
+ * no content hash for it and every source its symbols reference stayed
+ * "newer" after a clone or checkout, however many times sync ran.
+ *
+ * The manifest is adopted only when Git does not track it, no receipt covers
+ * it, and at least one symbol it declares is already in the compiled store
+ * (`isStored`): Kibi wrote it. A hand-written untracked manifest whose
+ * symbols the store never saw keeps the tracked-only boundary and sync's
+ * "stage this file" note. Returns whether a receipt was written.
+ */
+export declare function adoptUpsertOnlySymbolManifest(workspaceRoot: string, isStored: (ids: readonly string[]) => Promise<boolean>): Promise<boolean>;
 export {};
 //# sourceMappingURL=untracked-targets.d.ts.map

package/dist/commands/sync/untracked-targets.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"untracked-targets.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/untracked-targets.ts"],"names":[],"mappings":"AAyBA,UAAU,oBAAoB;IAC5B,YAAY,EAAE,CACZ,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,SAAS,MAAM,EAAE,EACvB,OAAO,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,KAC5D,MAAM,CAAC;IACZ,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC;IACtC,YAAY,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,MAAM,CAAC;CAC1D;AAQD;;;;;;;;;;;GAWG;AAEH,wBAAgB,4BAA4B,CAC1C,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,SAAS,MAAM,EAAE,EAC7B,IAAI,GAAE,OAAO,CAAC,oBAAoB,CAAM,GACvC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAsDrB"}
+{"version":3,"file":"untracked-targets.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/untracked-targets.ts"],"names":[],"mappings":"AA6BA,UAAU,oBAAoB;IAC5B,YAAY,EAAE,CACZ,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,SAAS,MAAM,EAAE,EACvB,OAAO,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,KAC5D,MAAM,CAAC;IACZ,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC;IACtC,YAAY,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,MAAM,CAAC;CAC1D;AAQD;;;;;;;;;;;GAWG;AAEH,wBAAgB,4BAA4B,CAC1C,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,SAAS,MAAM,EAAE,EAC7B,IAAI,GAAE,OAAO,CAAC,oBAAoB,CAAM,GACvC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAsDrB;AAED;;;;;;;;;;;;;;;GAeG;AAEH,wBAAsB,6BAA6B,CACjD,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,CAAC,GAAG,EAAE,SAAS,MAAM,EAAE,KAAK,OAAO,CAAC,OAAO,CAAC,GACrD,OAAO,CAAC,OAAO,CAAC,CAqBlB"}

package/dist/commands/sync/untracked-targets.js

@@ -20,7 +20,8 @@ import { createHash } from "node:crypto";
 import { existsSync, readFileSync } from "node:fs";
 import * as path from "node:path";
 import { load as parseYAML } from "js-yaml";
-import { isSymbolsManifestPath } from "../../utils/kb-paths.js";
+import { isUntrackedByGit, writePendingSourceReceipt, } from "../../operations/mutation/source-authoring.js";
+import { KB_PATHS, isSymbolsManifestPath } from "../../utils/kb-paths.js";
 const defaultDeps = {
     execFileSync: (file, args, options) => execFileSync(file, args, options),
     existsSync,
@@ -96,6 +97,47 @@ export function findUntrackedDocumentMatches(workspaceRoot, missingIds, deps = {
     }
     return matches;
 }
+/**
+ * Give an upsert-only symbol manifest the pending-source receipt kb_upsert
+ * writes since it learned to (`writeSourceForUpsert`).
+ *
+ * Older Kibi appended symbols to the untracked `.kb/symbols.yaml` that
+ * `kibi init` creates without a receipt. The upsert wrote those symbols into
+ * the store directly, but sync never saw the manifest, so the store recorded
+ * no content hash for it and every source its symbols reference stayed
+ * "newer" after a clone or checkout, however many times sync ran.
+ *
+ * The manifest is adopted only when Git does not track it, no receipt covers
+ * it, and at least one symbol it declares is already in the compiled store
+ * (`isStored`): Kibi wrote it. A hand-written untracked manifest whose
+ * symbols the store never saw keeps the tracked-only boundary and sync's
+ * "stage this file" note. Returns whether a receipt was written.
+ */
+// implements REQ-cli-status-pre-first-sync, REQ-core-persistence
+export async function adoptUpsertOnlySymbolManifest(workspaceRoot, isStored) {
+    const relative = KB_PATHS.symbolsManifest;
+    const absolute = path.resolve(workspaceRoot, relative);
+    if (!existsSync(absolute))
+        return false;
+    if (existsSync(pendingReceiptFor(workspaceRoot, relative)))
+        return false;
+    let bytes;
+    try {
+        bytes = readFileSync(absolute);
+    }
+    catch {
+        return false;
+    }
+    const ids = manifestIds(bytes.toString("utf8"));
+    if (ids.length === 0)
+        return false;
+    if (!isUntrackedByGit(workspaceRoot, relative))
+        return false;
+    if (!(await isStored(ids)))
+        return false;
+    writePendingSourceReceipt(workspaceRoot, relative, createHash("sha256").update(bytes).digest("hex"));
+    return true;
+}
 /** Where kb_upsert records the pending-source receipt of `relative`. */
 function pendingReceiptFor(workspaceRoot, relative) {
     return path.join(workspaceRoot, ".kb", "recovery", "pending-sources", `${createHash("sha256").update(relative).digest("hex")}.json`);

package/dist/commands/sync.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/commands/sync.ts"],"names":[],"mappings":"AA6BA,OAAO,KAAK,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AA6BjE,OAAO,EAEL,yBAAyB,EAE1B,MAAM,gDAAgD,CAAC;AAGxD,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAC7C,OAAO,EACL,KAAK,gBAAgB,EAGtB,MAAM,6BAA6B,CAAC;AAyBrC,OAAO,KAAK,EAAE,4BAA4B,EAAE,MAAM,qBAAqB,CAAC;AAkCxE,qBAAa,SAAU,SAAQ,KAAK;gBACtB,OAAO,EAAE,MAAM;CAI5B;AAmCD,wBAAgB,wBAAwB,CACtC,aAAa,EAAE,MAAM,EACrB,gBAAgB,EAAE,MAAM,EACxB,4BAA4B,UAAQ,EACpC,4BAA4B,GAAE,4BAA4B,EAAO,GAChE,MAAM,EAAE,CAuGV;AAiFD,MAAM,WAAW,UAAW,SAAQ,WAAW;IAC7C,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,UAAU,yBAAyB;IACjC,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,OAAO,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,OAAO,CAAC;CACvB;AAED,UAAU,kBAAkB;IAC1B,WAAW,CAAC,EAAE,CAAC,OAAO,EAAE,yBAAyB,KAAK,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IAC3E,UAAU,CAAC,EAAE,CACX,OAAO,EAAE,yBAAyB,GAAG;QAAE,UAAU,EAAE,OAAO,CAAA;KAAE,KACzD,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IAC1B,YAAY,CAAC,EAAE,CAAC,OAAO,EAAE;QAAE,OAAO,EAAE,MAAM,CAAA;KAAE,KAAK,aAAa,CAAC;IAC/D,yBAAyB,CAAC,EAAE,OAAO,yBAAyB,CAAC;CAC9D;AA+FD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,GAAG,IAAI,CAGvE;AAGD,wBAAgB,2BAA2B,CACzC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,IAAI,GAChB,IAAI,CAMN;AAED,wBAAgB,4BAA4B,CAC1C,WAAW,EAAE,UAAU,EAAE,EACzB,QAAQ,EAAE,OAAO,EACjB,OAAO,EAAE,OAAO,EAChB,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,IAAI,CAIN;AAED,wBAAgB,0BAA0B,CAAC,MAAM,EAAE;IACjD,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB,GAAG,IAAI,CAMP;AAED,wBAAgB,iCAAiC,CAC/C,WAAW,EAAE,UAAU,EAAE,EACzB,oBAAoB,EAAE,OAAO,EAC7B,iBAAiB,EAAE,MAAM,EACzB,WAAW,EAAE,MAAM,GAClB,IAAI,CAUN;AAGD,wBAAsB,WAAW,CAC/B,OAAO,GAAE;IACP,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,wBAAwB,CAAC,EAAE,OAAO,CAAC;IACnC,2EAA2E;IAC3E,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,wEAAwE;IACxE,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB;;;OAGG;IACH,gBAAgB,CAAC,EAAE,gBAAgB,CAAC;IACpC,uEAAuE;IACvE,KAAK,CAAC,EAAE,OAAO,CAAC;CACZ,EACN,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,UAAU,CAAC,CA+qCrB;AAED,OAAO,EAAE,qBAAqB,EAAE,MAAM,qBAAqB,CAAC"}

package/dist/commands/sync.js

@@ -33,10 +33,10 @@ import { loadEntityPaths } from "../utils/config.js";
 import { SYNC_CACHE_TTL_MS, SYNC_CACHE_VERSION, SYNC_COMPILER_FINGERPRINT, hashFile, hashManifestWithCoordinates, hashNormalized, readSyncCache, toCacheKey, writeSyncCache, } from "./sync/cache.js";
 import { clearRecoveredPendingSourceReceipts, discoverSourceFiles, } from "./sync/discovery.js";
 import { normalizeExtractionSources, processExtractions, } from "./sync/extraction.js";
-import { refreshManifestCoordinates } from "./sync/manifest.js";
+import { normalizeManifestLayout, refreshManifestCoordinates, } from "./sync/manifest.js";
 import { persistEntities, persistRelationships, retractEntitiesById, retractEntitiesForSources, retractEntityRelationshipsById, retractRelationships, } from "./sync/persistence.js";
 import { atomicPublish, atomicPublishGeneration, cleanupStaging, createUniqueStagingPath, prepareStagingEnvironment, } from "./sync/staging.js";
-import { findUntrackedDocumentMatches } from "./sync/untracked-targets.js";
+import { adoptUpsertOnlySymbolManifest, findUntrackedDocumentMatches, } from "./sync/untracked-targets.js";
 // Manual deletion of a written-but-unstaged source leaves a recovery receipt
 // behind; sync refuses to guess, so the error must name the way out.
 const PENDING_SOURCE_RECOVERY_HINT = " If the file was deleted on purpose, run 'kibi branch recover --apply' to rebuild the branch KB from the sources that remain.";
@@ -202,6 +202,32 @@ async function checkpointNoopSync(workspaceRoot, branch) {
         await engine.terminate();
     }
 }
+/** Whether the branch's compiled store already holds any of `ids`. */
+// implements REQ-cli-status-pre-first-sync
+async function storeHoldsAnyEntity(workspaceRoot, branch, ids) {
+    const engine = new EngineClient({
+        workspaceRoot,
+        branch,
+        timeout: 120_000,
+    });
+    try {
+        await engine.start();
+        for (const id of ids) {
+            const found = await engine.queryEntities({ id, limit: 1, offset: 0 });
+            if (found.count > 0 || found.entities.length > 0)
+                return true;
+        }
+        return false;
+    }
+    catch {
+        // Adoption is best effort: an unreadable store adopts nothing and the
+        // compile below reports the store itself.
+        return false;
+    }
+    finally {
+        await engine.terminate();
+    }
+}
 function compilerCacheHasEntityDelta(cache) {
     return (cache.entityHashes !== undefined && cache.sourceEntityIds !== undefined);
 }
@@ -354,6 +380,18 @@ export async function syncCommand(options = {}, runtime = {}) {
             ensureBranchStoreManifest(workspaceRoot, currentBranch);
             await ensureJournaledBranchStoreAsync(livePathForEngine);
         }
+        // implements REQ-cli-status-pre-first-sync
+        // An untracked symbol manifest that only kb_upsert ever wrote (older Kibi
+        // left it without a pending-source receipt) gets the receipt here, so
+        // this sync compiles it and records its content hash. Without it the
+        // sources its symbols reference read as newer after every clone.
+        if (!validateOnly &&
+            recoveryBackupPath === undefined &&
+            options.detachedSnapshot === undefined &&
+            runtime.createProlog === undefined) {
+            const branch = currentBranch;
+            await adoptUpsertOnlySymbolManifest(workspaceRoot, (ids) => storeHoldsAnyEntity(workspaceRoot, branch, ids));
+        }
         const needsExclusiveGenerationPublish = !validateOnly && (rebuild || recoveryBackupPath !== undefined);
         if (needsExclusiveGenerationPublish) {
             // Recovery intentionally avoids attaching the broken live store. The
@@ -413,6 +451,17 @@ export async function syncCommand(options = {}, runtime = {}) {
         const relationshipShardFiles = existsSync(relationshipsDir)
             ? trackedRelationshipFiles(workspaceRoot, relationshipsDir, recoveryBackupPath !== undefined, recoveredPendingReceiptPaths)
             : [];
+        // A manifest an older writer left in flow layout is rewritten as block
+        // YAML before anything hashes it, ahead of the no-op fast path below, so
+        // a project whose cache is already fresh still gets it on the next sync.
+        if (!validateOnly) {
+            for (const file of manifestFiles) {
+                const normalized = normalizeManifestLayout(file);
+                if (normalized !== null) {
+                    console.log(`\u2713 Rewrote ${path.relative(workspaceRoot, file)} in block layout (${normalized} symbol${normalized === 1 ? "" : "s"})`);
+                }
+            }
+        }
         // No-op is a first-class compiler result. Hashing the configured inputs is
         // sufficient when normalized entity/shard inventories are already fresh;
         // avoid rebuilding maps and rediscovering RDF state for the common path.

package/dist/engine.d.ts.map

@@ -1 +1 @@
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package/dist/engine.js

@@ -18,7 +18,7 @@ import { kibiPackageVersions } from "./package-versions.js";
 import { writePerformanceTraceEvent } from "./performance-trace.js";
 import { PrologProcess, resolveKbPlPath } from "./prolog.js";
 import { parseEntityFromList, parseListOfLists } from "./prolog/codec.js";
-import { retryAttachAfterBreakingStaleLock } from "./prolog/store-lock.js";
+import { decideStoreLockTakeover, isProcessAlive, noteDeadHolderBeforeAttach, readRdfLockPid, readStoreLockOwner, recordStoreLockTakeover, retryAttachAfterBreakingStaleLock, } from "./prolog/store-lock.js";
 import { resolveSwipl, swiplIdentity } from "./prolog/swipl-resolver.js";
 import { queryEntityChunks } from "./public/operations/discovery-entities.js";
 import { isValidBranchName } from "./utils/branch-resolver.js";
@@ -632,35 +632,41 @@ function releaseStartLock(lockPath, descriptor) {
         // Another starter may already have cleaned the lock.
     }
 }
+// implements REQ-core-journaled-engine-persistence
 function recoverStaleJournalLock(branchPath) {
     const lockPath = path.join(branchPath, "rdf", "lock");
     if (!existsSync(lockPath))
         return;
-    let contents = "";
-    try {
-        contents = readFileSync(lockPath, "utf8");
-    }
-    catch {
+    const pid = readRdfLockPid(lockPath);
+    if (pid === null || pid === process.pid)
         return;
+    let reason;
+    if (!isProcessAlive(pid)) {
+        reason = decideStoreLockTakeover({ pid }).reason;
+    }
+    else {
+        // A live pid still loses the lock when the lock and its journal were
+        // copied in from another workspace: that pid holds the original store,
+        // never this copy.
+        const journal = readStoreLockOwner(branchPath)?.owner ?? null;
+        if (journal === null || journal.pid !== pid)
+            return;
+        const decision = decideStoreLockTakeover(journal, {
+            storePath: branchPath,
+        });
+        if (decision.action !== "break")
+            return;
+        reason = decision.reason;
     }
-    const match = /pid\((\d+)\)/.exec(contents);
-    if (!match)
-        return;
-    const pid = Number.parseInt(match[1] ?? "", 10);
-    if (!Number.isFinite(pid) || pid <= 0 || pid === process.pid)
-        return;
+    // Breaking a stale holder's lock is a takeover; record it for kb_status
+    // and kibi doctor instead of healing silently.
+    recordStoreLockTakeover(branchPath, pid, reason);
     try {
-        process.kill(pid, 0);
-        return;
+        rmSync(lockPath, { force: true });
     }
     catch {
-        try {
-            rmSync(lockPath, { force: true });
-        }
-        catch {
-            // Let rdf_attach_db report the lock error if another process wins the
-            // race between the liveness probe and removal.
-        }
+        // Let rdf_attach_db report the lock error if another process wins the
+        // race between the liveness probe and removal.
     }
 }
 function daemonEntry() {
@@ -1565,8 +1571,13 @@ export class EngineSession {
     }
     async boot() {
         await this.prolog.start();
+        // A killed holder never makes kb_attach fail (its OS lock died with it),
+        // so a dead-holder takeover must be noted before the attach succeeds.
+        const recordTakeover = noteDeadHolderBeforeAttach(this.branchPath);
         const attached = await this.prolog.query(`kb_attach('${quoteProlog(this.branchPath)}')`);
-        if (!attached.success) {
+        if (attached.success)
+            recordTakeover();
+        else {
             // The daemon hosts the branch store for every later request, so a
             // store-locked startup with a provably dead holder is auto-healed here
             // exactly like the CLI runtime path; live holders abort the startup

package/dist/intent-search.d.ts

@@ -42,6 +42,13 @@ export type IntentSearchAnalysis = Readonly<{
     acceptedCount: number;
     topScore: number | null;
     topTwoMargin: number | null;
+    /**
+     * Margin between the top match and the best match it is not linked to in
+     * the traceability graph. A requirement and its own scenario, facts or
+     * tests tie without competing, so `ambiguous` reads this margin, not
+     * `topTwoMargin`.
+     */
+    topRivalMargin: number | null;
     abstained: boolean;
     ambiguous: boolean;
 }>;

package/dist/intent-search.d.ts.map

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