kibi-cli 2.17.0 → 2.19.0

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";

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",

package/dist/cli-register-proof.js

@@ -162,7 +162,15 @@ function renderInspection(result) {
     if (inspection.ciWorkflows.length > 0)
         lines.push(`CI workflows: ${inspection.ciWorkflows.join(", ")}`);
     lines.push("");
-    lines.push(`Current integration: ${inspection.currentIntegration ?? "none"}`);
+    const configured = inspection.currentIntegrations ?? [];
+    if (configured.length === 0) {
+        lines.push(`Current integration: ${inspection.currentIntegration ?? "none"}`);
+    }
+    else {
+        lines.push("Current integrations:");
+        for (const entry of configured)
+            lines.push(`  ${entry.id} (${entry.producer}: ${entry.command.join(" ")})`);
+    }
     lines.push("");
     lines.push(`Recommendation: ${inspection.recommendation}`);
     if (inspection.missing.length > 0) {

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

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AA2FA,MAAM,WAAW,aAAa;IAC5B,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC3B;AAGD,wBAAsB,aAAa,CACjC,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAmH/B;AAED,wBAAsB,4BAA4B,CAChD,IAAI,GAAE,MAAM,OAAO,CAAC;IAAE,gBAAgB,CAAC,EAAE,OAAO,CAAA;CAAE,CACT,GACxC,OAAO,CAAC,OAAO,CAAC,CAOlB;AAED,wBAAsB,uBAAuB,CAC3C,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;;;;;;;;;;;;;;;;MAkE3C;AAkGD,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAGzE;AAED,wBAAgB,2BAA2B,CACzC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,GACX,MAAM,GAAG,SAAS,CAepB"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AA4FA,MAAM,WAAW,aAAa;IAC5B,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC3B;AAGD,wBAAsB,aAAa,CACjC,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAmH/B;AAED,wBAAsB,4BAA4B,CAChD,IAAI,GAAE,MAAM,OAAO,CAAC;IAAE,gBAAgB,CAAC,EAAE,OAAO,CAAA;CAAE,CACT,GACxC,OAAO,CAAC,OAAO,CAAC,CAOlB;AAED,wBAAsB,uBAAuB,CAC3C,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;;;;;;;;;;;;;;;;MAkE3C;AAkGD,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAGzE;AAED,wBAAgB,2BAA2B,CACzC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,GACX,MAAM,GAAG,SAAS,CAepB"}

package/dist/commands/doctor.js

@@ -26,7 +26,7 @@ import { describeConfiguredCapabilityPlugins, readProjectKibiConfig, } from "../
 import { SwiplResolutionError, inspectSwiplBundle, probeRequiredLibraries, resolveSwipl, } from "../prolog/swipl-resolver.js";
 import { buildMigrationPlan, migrationAction, } from "../public/operations/migration-plan.js";
 import { resolveBranchAttachment, resolveReadBranchAttachment, } from "../utils/branch-resolver.js";
-import { branchStoreCompilation, inspectBranchStore, uncompiledBranchStoreReason, } from "../utils/branch-store.js";
+import { branchStoreCompilation, inspectBranchStore, storeLockTakeoverReason, uncompiledBranchStoreReason, } from "../utils/branch-store.js";
 import { resolveGitRepository, } from "../utils/git-repository-context.js";
 import { readKbManifestStatus } from "../utils/kb-manifest.js";
 import { hasManagedHooks, outdatedManagedHooks } from "./init-helpers.js";
@@ -692,29 +692,41 @@ 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})` : ""}`,
-            details: { ...details, generation: compilation.generation },
+            message: withTakeover(`Compiled for ${branch}${compilation.generation ? ` (${compilation.generation})` : ""}`),
+            details: {
+                ...details,
+                generation: compilation.generation,
+                ...takeoverDetails,
+            },
         };
     }
     const reason = uncompiledBranchStoreReason(workspaceRoot, store, branch);
     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/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":"AAsBA,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,CAiDrB"}
+{"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

@@ -16,8 +16,12 @@
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
  */
 import { execFileSync } from "node:child_process";
+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 { 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,
@@ -62,11 +66,20 @@ export function findUntrackedDocumentMatches(workspaceRoot, missingIds, deps = {
     for (const relative of untracked) {
         if (remaining.size === 0)
             break;
-        if (!relative.endsWith(".md"))
+        const normalized = relative.replaceAll("\\", "/");
+        const manifest = isSymbolsManifestPath(normalized);
+        if (!normalized.endsWith(".md") && !manifest)
             continue;
-        const absolute = path.resolve(workspaceRoot, relative.replaceAll("\\", "/"));
+        const absolute = path.resolve(workspaceRoot, normalized);
         if (!resolved.existsSync(absolute))
             continue;
+        const workspaceRelative = path
+            .relative(workspaceRoot, absolute)
+            .replaceAll("\\", "/");
+        // A pending-source receipt makes an untracked file visible to sync, so
+        // the file cannot be why an id is missing.
+        if (existsSync(pendingReceiptFor(workspaceRoot, workspaceRelative)))
+            continue;
         let content;
         try {
             content = resolved.readFileSync(absolute, "utf8");
@@ -74,17 +87,76 @@ export function findUntrackedDocumentMatches(workspaceRoot, missingIds, deps = {
         catch {
             continue;
         }
-        const id = frontmatterId(content);
-        if (id !== null && remaining.has(id)) {
-            const workspaceRelative = path
-                .relative(workspaceRoot, absolute)
-                .replaceAll("\\", "/");
-            matches.set(id, workspaceRelative);
-            remaining.delete(id);
+        const ids = manifest ? manifestIds(content) : [frontmatterId(content)];
+        for (const id of ids) {
+            if (id !== null && remaining.has(id)) {
+                matches.set(id, workspaceRelative);
+                remaining.delete(id);
+            }
         }
     }
     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`);
+}
+/** Symbol ids declared by an untracked symbols manifest. */
+function manifestIds(content) {
+    try {
+        const parsed = parseYAML(content);
+        const symbols = Array.isArray(parsed?.symbols) ? parsed.symbols : [];
+        return symbols.flatMap((symbol) => symbol !== null &&
+            typeof symbol === "object" &&
+            typeof symbol.id === "string"
+            ? [symbol.id]
+            : []);
+    }
+    catch {
+        return [];
+    }
+}
 /**
  * Extract `id:` from a markdown document's YAML frontmatter (the first
  * `---` block). Documents whose id never appears in the frontmatter region

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

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package/dist/commands/sync.js

@@ -33,9 +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 { 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.";
@@ -201,9 +202,58 @@ 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);
 }
+/**
+ * Name every dangling relationship and its missing endpoint, and say when an
+ * endpoint is declared in a source sync cannot see (untracked by Git and
+ * without a pending-source receipt): staging that file is the fix.
+ */
+// implements REQ-core-persistence
+function reportDanglingRelationships(workspaceRoot, validationErrors) {
+    console.warn(`Warning: ${validationErrors.length} dangling relationship(s) found`);
+    const missing = new Set();
+    for (const { relationship, error } of validationErrors) {
+        const endpoint = error === "missing_from" ? relationship.from : relationship.to;
+        missing.add(endpoint);
+        console.warn(`  - ${error}: ${relationship.type} ${relationship.from} -> ${relationship.to} (${endpoint} is not in this branch's sources)`);
+    }
+    const untracked = findUntrackedDocumentMatches(workspaceRoot, [...missing]);
+    const byFile = new Map();
+    for (const [id, file] of untracked) {
+        byFile.set(file, [...(byFile.get(file) ?? []), id]);
+    }
+    for (const [file, ids] of byFile) {
+        console.warn(`  Note: ${ids.sort().join(", ")} ${ids.length === 1 ? "is" : "are"} declared in ${file}, which Git does not track and no pending-source receipt covers, so sync ignores it. Run \`git add ${file}\` (staging is enough) or rewrite the entity with kb_upsert, then sync again.`);
+    }
+}
 function compilerCacheIsFresh(cache, workspaceRoot, sourceFiles, nowMs) {
     const sourceKeys = sourceFiles.map((file) => toCacheKey(workspaceRoot, file));
     if (Object.keys(cache.hashes).some((key) => !sourceKeys.includes(key))) {
@@ -330,6 +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
@@ -389,6 +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.
@@ -852,7 +925,7 @@ export async function syncCommand(options = {}, runtime = {}) {
                     ? []
                     : validateRelationships(allRelationships, entityIds);
                 if (validationErrors.length > 0) {
-                    console.warn(`Warning: ${validationErrors.length} dangling relationship(s) found`);
+                    reportDanglingRelationships(workspaceRoot, validationErrors);
                 }
                 const danglingKeys = new Set(validationErrors.map(({ relationship }) => `${relationship.type}|${relationship.from}|${relationship.to}`));
                 const shardDeltaByKey = new Map();
@@ -973,10 +1046,7 @@ export async function syncCommand(options = {}, runtime = {}) {
             const { entityCount, kbModified: entitiesModified } = await persistEntities(prolog, results, entityIds);
             const validationErrors = validateRelationships(allRelationships, entityIds);
             if (validationErrors.length > 0) {
-                console.warn(`Warning: ${validationErrors.length} dangling relationship(s) found`);
-                for (const { relationship, error } of validationErrors) {
-                    console.warn(`  - ${error}: ${relationship.type} ${relationship.from} -> ${relationship.to}`);
-                }
+                reportDanglingRelationships(workspaceRoot, validationErrors);
             }
             const danglingKeys = new Set(validationErrors.map(({ relationship: r }) => `${r.type}|${r.from}|${r.to}`));
             const validRelationships = allRelationships.filter((r) => !danglingKeys.has(`${r.type}|${r.from}|${r.to}`));

package/dist/engine.d.ts

@@ -8,6 +8,10 @@ export { EngineQueryLimitError, QUERY_LIMIT_EXCEEDED_CODE, queryLimitExceededOf,
 export type { EngineLimitExceeded, EngineQueryLimits, } from "./engine-limits.js";
 export declare const ENGINE_PROTOCOL_VERSION = 1;
 export declare const ENGINE_IDLE_TIMEOUT_MS: number;
+/** Upper bound between two wall-clock idle checks of the engine daemon. */
+export declare const ENGINE_IDLE_CHECK_INTERVAL_MS: number;
+/** How long a stopping daemon waits for SWI to halt on stdin EOF. */
+export declare const ENGINE_PROLOG_EXIT_GRACE_MS = 1000;
 /**
  * Package versions this engine build carries (KIBI_PACKAGE_VERSIONS when
  * set). The client sends them on every request and the daemon reports its

package/dist/engine.d.ts.map

@@ -1 +1 @@
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