kibi-cli 2.16.0 → 2.18.0

package/dist/cli-protocol.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli-protocol.d.ts","sourceRoot":"","sources":["../src/cli-protocol.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AAG7D,OAAO,EACL,KAAK,mBAAmB,EAEzB,MAAM,mBAAmB,CAAC;AAS3B,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAE7E,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAMpE,MAAM,MAAM,UAAU,GAAG,gBAAgB,GAAG;IAC1C,QAAQ,CAAC,mBAAmB,CAAC,EAAE,mBAAmB,CAAC;CACpD,CAAC;AAGF,MAAM,MAAM,iBAAiB,GAAG;IAC9B,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;CAC1B,CAAC;AAEF,iBAAS,WAAW,CAClB,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,UAAU,GAAG,cAAc,EAClC,IAAI,CAAC,EAAE;IACL,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,SAAS,eAAe,EAAE,CAAC;IACpC,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB,EACD,SAAS,UAAO,EAChB,OAAO,CAAC,EAAE,OAAO,GAChB,iBAAiB,CAwBnB;AA4BD;;;;GAIG;AAEH,wBAAgB,iBAAiB,CAC/B,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE,UAAU,CAAC,OAAO,WAAW,CAAC,CAAC,CAAC,CAAC,EACvC,KAAK,EAAE,OAAO,GACb,iBAAiB,CAWnB;AAGD,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,OAAO,EACd,OAAO,EAAE,UAAU,GAClB,OAAO,CAAC,iBAAiB,CAAC,CAwE5B"}
+{"version":3,"file":"cli-protocol.d.ts","sourceRoot":"","sources":["../src/cli-protocol.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AAG7D,OAAO,EACL,KAAK,mBAAmB,EAEzB,MAAM,mBAAmB,CAAC;AAS3B,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAE7E,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAMpE,MAAM,MAAM,UAAU,GAAG,gBAAgB,GAAG;IAC1C,QAAQ,CAAC,mBAAmB,CAAC,EAAE,mBAAmB,CAAC;CACpD,CAAC;AAGF,MAAM,MAAM,iBAAiB,GAAG;IAC9B,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;CAC1B,CAAC;AAEF,iBAAS,WAAW,CAClB,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,UAAU,GAAG,cAAc,EAClC,IAAI,CAAC,EAAE;IACL,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,SAAS,eAAe,EAAE,CAAC;IACpC,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB,EACD,SAAS,UAAO,EAChB,OAAO,CAAC,EAAE,OAAO,GAChB,iBAAiB,CAwBnB;AA4BD;;;;GAIG;AAEH,wBAAgB,iBAAiB,CAC/B,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE,UAAU,CAAC,OAAO,WAAW,CAAC,CAAC,CAAC,CAAC,EACvC,KAAK,EAAE,OAAO,GACb,iBAAiB,CAWnB;AAGD,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,OAAO,EACd,OAAO,EAAE,UAAU,GAClB,OAAO,CAAC,iBAAiB,CAAC,CAqF5B"}

package/dist/cli-protocol.js

@@ -78,6 +78,19 @@ export async function executeOperation(catalogName, input, context) {
         if (!protocolValid(spec, envelope)) {
             return errorResult(catalogName, new OperationError("PROTOCOL_VALIDATION_FAILED", "Operation produced a result that does not satisfy its generated output contract."), spec);
         }
+        // A result the operation itself reports as an error (a rejected
+        // bootstrap, a refused migration plan) exits non-zero like any other.
+        if (envelope.status === "error") {
+            return {
+                exitCode: 1,
+                stdout: `${JSON.stringify(envelope)}\n`,
+                ...(envelope.error
+                    ? {
+                        stderr: `Error [${envelope.error.code}]: ${envelope.error.message}\n`,
+                    }
+                    : {}),
+            };
+        }
         return { exitCode: 0, stdout: `${JSON.stringify(envelope)}\n` };
     }
     catch (error) {

package/dist/cli-register-proof.d.ts

@@ -1,3 +1,9 @@
 import type { Command } from "commander";
 export declare function registerProofCommand(program: Command): void;
+/**
+ * `--command` for `kibi proof inspect`: a JSON array of argv strings, or
+ * space-separated words (no shell quoting; Kibi runs integrations with
+ * `shell: false`).
+ */
+export declare function parseCommandOption(value: string): readonly string[];
 //# sourceMappingURL=cli-register-proof.d.ts.map

package/dist/cli-register-proof.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli-register-proof.d.ts","sourceRoot":"","sources":["../src/cli-register-proof.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAIzC,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CA6L3D"}
+{"version":3,"file":"cli-register-proof.d.ts","sourceRoot":"","sources":["../src/cli-register-proof.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAIzC,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CA2M3D;AAED;;;;GAIG;AAEH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,SAAS,MAAM,EAAE,CAwBnE"}

package/dist/cli-register-proof.js

@@ -41,9 +41,16 @@ export function registerProofCommand(program) {
         .command("inspect")
         .description("Detect test infrastructure, propose a proof integration and return the reviewed plan that writes .kb/proof/integrations.json")
         .option("--update <id>", "Plan adding or replacing this integration in an existing .kb/proof/integrations.json")
+        .option("--command <command>", 'Command the proposed integration runs instead of the detected one: space-separated words, or a JSON array of argv strings (e.g. \'["npx","vitest","run","tests/e2e"]\')')
         .option("--json", "Emit structured JSON", false)
         .action(withExitCode(async (options) => {
-        const result = await (await import("./proof/inspect.js")).inspectProofEnvironment(process.cwd(), options.update === undefined ? {} : { update: options.update });
+        const command = options.command === undefined
+            ? undefined
+            : parseCommandOption(options.command);
+        const result = await (await import("./proof/inspect.js")).inspectProofEnvironment(process.cwd(), {
+            ...(options.update === undefined ? {} : { update: options.update }),
+            ...(command === undefined ? {} : { command }),
+        });
         if (options.json) {
             process.stdout.write(`${JSON.stringify(result, null, 2)}\n`);
             return undefined;
@@ -109,6 +116,33 @@ export function registerProofCommand(program) {
         });
     }));
 }
+/**
+ * `--command` for `kibi proof inspect`: a JSON array of argv strings, or
+ * space-separated words (no shell quoting; Kibi runs integrations with
+ * `shell: false`).
+ */
+// implements REQ-kibi-verification-evidence-contract
+export function parseCommandOption(value) {
+    const trimmed = value.trim();
+    if (trimmed.startsWith("[")) {
+        let parsed;
+        try {
+            parsed = JSON.parse(trimmed);
+        }
+        catch {
+            throw new Error("--command must be a JSON array of argv strings or space-separated words.");
+        }
+        if (!Array.isArray(parsed) ||
+            parsed.length === 0 ||
+            !parsed.every((entry) => typeof entry === "string" && entry !== ""))
+            throw new Error("--command must be a JSON array of non-empty argv strings.");
+        return parsed;
+    }
+    const words = trimmed.split(/\s+/).filter((word) => word !== "");
+    if (words.length === 0)
+        throw new Error("--command must not be empty.");
+    return words;
+}
 function renderInspection(result) {
     const inspection = result;
     const lines = ["Proof environment", ""];
@@ -128,7 +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) {
@@ -145,6 +187,8 @@ function renderInspection(result) {
     if (inspection.integrationPlan) {
         const plan = inspection.integrationPlan;
         lines.push(`Integration plan: ${plan.planHash.slice(0, 12)} (actions: ${plan.actions.map((action) => action.id).join(", ")}); rerun with --json for the plan to pass to kb_apply_plan.`);
+        if (inspection.integrationPlanReason)
+            lines.push(inspection.integrationPlanReason);
     }
     else if (inspection.integrationPlanReason) {
         lines.push("");

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";
@@ -692,11 +692,17 @@ function checkBranchStore() {
         };
     }
     const compilation = branchStoreCompilation(store);
+    // implements REQ-core-journaled-engine-persistence
+    const takeover = storeLockTakeoverReason(store.path);
     if (compilation.compiled) {
         return {
             passed: true,
-            message: `Compiled for ${branch}${compilation.generation ? ` (${compilation.generation})` : ""}`,
-            details: { ...details, generation: compilation.generation },
+            message: `Compiled for ${branch}${compilation.generation ? ` (${compilation.generation})` : ""}${takeover ? `. ${String(takeover.detail)}` : ""}`,
+            details: {
+                ...details,
+                generation: compilation.generation,
+                ...(takeover ? { lockTakeover: takeover } : {}),
+            },
         };
     }
     const reason = uncompiledBranchStoreReason(workspaceRoot, store, branch);

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":"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"}

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

@@ -16,8 +16,11 @@
  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 { isSymbolsManifestPath } from "../../utils/kb-paths.js";
 const defaultDeps = {
     execFileSync: (file, args, options) => execFileSync(file, args, options),
     existsSync,
@@ -62,11 +65,20 @@ 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 +86,35 @@ 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;
 }
+/** 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

@@ -1 +1 @@
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package/dist/commands/sync.js

@@ -36,6 +36,7 @@ import { normalizeExtractionSources, processExtractions, } from "./sync/extracti
 import { 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";
 // 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.";
@@ -204,6 +205,29 @@ async function checkpointNoopSync(workspaceRoot, branch) {
 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))) {
@@ -852,7 +876,7 @@ 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 +997,7 @@ 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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package/dist/engine.js

@@ -34,6 +34,10 @@ const READ_LIMITED_METHODS = new Set([
 ]);
 export const ENGINE_PROTOCOL_VERSION = 1;
 export const ENGINE_IDLE_TIMEOUT_MS = 10 * 60 * 1000;
+/** Upper bound between two wall-clock idle checks of the engine daemon. */
+export const ENGINE_IDLE_CHECK_INTERVAL_MS = 30 * 1000;
+/** How long a stopping daemon waits for SWI to halt on stdin EOF. */
+export 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
@@ -1695,7 +1699,12 @@ export async function runEngineDaemon(requestedOptions) {
     writeFileSync(enginePidPath(options.workspaceRoot, options.branch), `${process.pid}\n`, { mode: 0o600 });
     const server = net.createServer();
     let activeClients = 0;
-    let idleTimer = null;
+    // implements REQ-core-journaled-engine-persistence
+    // Idle exit compares wall-clock time: a one-shot timer does not advance
+    // while the host (a VM, a laptop) is suspended, so a daemon would outlive
+    // its idle budget by the whole suspension.
+    let lastActivityAt = Date.now();
+    let idleWatch = null;
     let queue = Promise.resolve();
     let idleCompactionQueued = false;
     const queryCache = new Map();
@@ -1783,12 +1792,17 @@ export async function runEngineDaemon(requestedOptions) {
                 idleCompactionQueued = false;
             });
         }
-        if (idleTimer)
-            clearTimeout(idleTimer);
-        idleTimer = setTimeout(() => {
-            if (activeClients === 0)
+        lastActivityAt = Date.now();
+        if (idleWatch)
+            return;
+        const idleMs = engineIdleTimeoutMs();
+        idleWatch = setInterval(() => {
+            if (!shuttingDown &&
+                activeClients === 0 &&
+                Date.now() - lastActivityAt >= idleMs)
                 void shutdown();
-        }, engineIdleTimeoutMs());
+        }, Math.min(idleMs, ENGINE_IDLE_CHECK_INTERVAL_MS));
+        idleWatch.unref();
     };
     const handle = async (request, cancelledRequests) => {
         if (request.protocolVersion !== ENGINE_PROTOCOL_VERSION) {
@@ -2121,8 +2135,8 @@ export async function runEngineDaemon(requestedOptions) {
         shuttingDown = true;
         process.off("SIGTERM", requestSignalShutdown);
         process.off("SIGINT", requestSignalShutdown);
-        if (idleTimer)
-            clearTimeout(idleTimer);
+        if (idleWatch)
+            clearInterval(idleWatch);
         clearInterval(workspaceWatchdog);
         // Stop accepting clients before the first asynchronous durability step.
         // Keep the PID published until Prolog releases the branch-store lock.
@@ -2131,6 +2145,7 @@ export async function runEngineDaemon(requestedOptions) {
         const saved = session.needsRecycle()
             ? null
             : await prolog.query("kb_save").catch(() => null);
+        let detached = false;
         if (saved?.success) {
             try {
                 fsyncJournaledBranchStore(branchPath);
@@ -2139,8 +2154,22 @@ export async function runEngineDaemon(requestedOptions) {
                 // Shutdown remains best effort. Request-time writes fail closed if
                 // their durability barrier cannot complete.
             }
-        }
-        await prolog.terminate().catch(() => undefined);
+            // implements REQ-core-journaled-engine-persistence
+            // Release the store the way the one-shot path does: kb_detach removes
+            // rdf/lock and the ownership journal. A SIGTERM'd SWI process never
+            // runs its at_halt cleanup, so skipping this left a dead lock behind
+            // on every stop.
+            detached = await prolog
+                .query("kb_detach")
+                .then((result) => result.success)
+                .catch(() => false);
+        }
+        // Once kb_detach released the store, nothing in at_halt is needed and the
+        // child is signalled at once. Otherwise let SWI halt on stdin EOF (running
+        // its at_halt cleanup) for a bounded moment; the wait ends on exit.
+        await prolog
+            .terminate({ graceMs: detached ? 0 : ENGINE_PROLOG_EXIT_GRACE_MS })
+            .catch(() => undefined);
         for (const client of clients)
             client.destroy();
         // A close callback can remain pending on older Node releases when a
@@ -2189,6 +2218,7 @@ export async function runEngineDaemon(requestedOptions) {
                 const bytes = typeof chunk === "string" ? Buffer.from(chunk) : chunk;
                 buffer = parseFrames(Buffer.concat([buffer, bytes]), (value) => {
                     const request = value;
+                    lastActivityAt = Date.now();
                     if (shuttingDown) {
                         writeSocketFrame(socket, {
                             id: request.id,

package/dist/operations/modeling/predicate-applicability.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"predicate-applicability.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-applicability.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,KAAK,qBAAqB,EAE3B,MAAM,uBAAuB,CAAC;AAG/B,eAAO,MAAM,uBAAuB,OAAO,CAAC;AAC5C,eAAO,MAAM,0BAA0B,MAAM,CAAC;AAC9C,eAAO,MAAM,qBAAqB,OAAO,CAAC;AAqW1C,MAAM,WAAW,qBAAqB;IACpC,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC;IAC3B,QAAQ,CAAC,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;IACpC,QAAQ,CAAC,kBAAkB,EAAE,MAAM,CAAC;CACrC;AAED;;;;GAIG;AACH,wBAAgB,6BAA6B,CAC3C,MAAM,EAAE,qBAAqB,EAC7B,IAAI,EAAE,MAAM,GACX,qBAAqB,CA2EvB"}
+{"version":3,"file":"predicate-applicability.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-applicability.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,KAAK,qBAAqB,EAE3B,MAAM,uBAAuB,CAAC;AAG/B,eAAO,MAAM,uBAAuB,OAAO,CAAC;AAC5C,eAAO,MAAM,0BAA0B,MAAM,CAAC;AAC9C,eAAO,MAAM,qBAAqB,OAAO,CAAC;AA8W1C,MAAM,WAAW,qBAAqB;IACpC,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC;IAC3B,QAAQ,CAAC,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;IACpC,QAAQ,CAAC,kBAAkB,EAAE,MAAM,CAAC;CACrC;AAED;;;;GAIG;AACH,wBAAgB,6BAA6B,CAC3C,MAAM,EAAE,qBAAqB,EAC7B,IAAI,EAAE,MAAM,GACX,qBAAqB,CA2EvB"}

package/dist/operations/modeling/predicate-applicability.js

@@ -2,7 +2,10 @@ import { usageHintsForSchema, } from "./predicate-ranker.js";
 export const MIN_APPLICABILITY_SCORE = 0.62;
 export const STRONG_APPLICABILITY_SCORE = 0.8;
 export const WEAK_CANDIDATE_MARGIN = 0.06;
-const NORMATIVE_OR_VALIDITY_PATTERN = /\b(?:must|shall|should|required|requires?|may\s+only|only\s+.+?\s+(?:may|can)|must\s+not|shall\s+not|cannot|can't|allowed|denied|forbidden|prohibited|invalid|unresolved|reject(?:s|ed|ion)?|fail(?:s|ed|ure)?\s+(?:clearly|explicitly|with)|defaults?\s+to|states?\s+are|owned\s+by|initializes?\s+after|before|unless|when|if|(?:exception|exempt)\s+(?:to|from|when|if|unless))\b/i;
+// A bare permission modal ("coaches can read", "users may export", "are
+// permitted to") states a permission as much as "allowed" does, so it must
+// reach the permission_rule intent rule instead of being rejected here.
+const NORMATIVE_OR_VALIDITY_PATTERN = /\b(?:must|shall|should|required|requires?|may\s+only|only\s+.+?\s+(?:may|can)|(?:can|may)\s+(?:not\s+)?(?:only\s+)?\w+|(?:is|are)\s+(?:not\s+)?(?:allowed|permitted)\s+to|permitted|must\s+not|shall\s+not|cannot|can't|allowed|denied|forbidden|prohibited|invalid|unresolved|reject(?:s|ed|ion)?|fail(?:s|ed|ure)?\s+(?:clearly|explicitly|with)|defaults?\s+to|states?\s+are|owned\s+by|initializes?\s+after|before|unless|when|if|(?:exception|exempt)\s+(?:to|from|when|if|unless))\b/i;
 function expressesNormativeOrValidityIntent(text) {
     return /^\s*no\b/i.test(text) || NORMATIVE_OR_VALIDITY_PATTERN.test(text);
 }
@@ -95,8 +98,14 @@ const INTENT_RULES = {
     },
     permission_rule: {
         allOf: [
-            [/only|may|can|allowed|denied|forbidden|must\s+not|cannot/i],
-            [/delete|export|access|read|write|update|remove|manage|permission/i],
+            [/only|may|can|allowed|permitted|denied|forbidden|must\s+not|cannot/i],
+            [
+                /delete|export|access|read|write|update|remove|manage|permission/i,
+                // A common action verb counts only right after the permission modal
+                // ("must not publish", "may approve"), so a quota such as "uploads
+                // must not exceed 10 MB" does not read as a permission.
+                /\b(?:may|can|cannot|can't|must\s+(?:not|never)|never|(?:is|are)\s+(?:not\s+)?(?:allowed|permitted|forbidden)\s+to)\s+(?:only\s+)?(?:publish|unpublish|approve|assign|view|see|edit|modify|create|submit|share|invite|upload|download|comment|post|complete|archive|restore|grant|revoke|purchase|cancel|execute|invoke|configure|moderate|ban|join|book|reserve|transfer|close|reopen|merge)\b/i,
+            ],
         ],
     },
     resource_constraint: {

package/dist/operations/modeling/predicate-catalog-4.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"predicate-catalog-4.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-catalog-4.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,sBAAsB,CAAC;AAGrE,eAAO,MAAM,mBAAmB,EAAE,wBAAwB,EAqTzD,CAAC"}
+{"version":3,"file":"predicate-catalog-4.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-catalog-4.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,sBAAsB,CAAC;AAGrE,eAAO,MAAM,mBAAmB,EAAE,wBAAwB,EAyTzD,CAAC"}

package/dist/operations/modeling/predicate-catalog-4.js

@@ -203,10 +203,14 @@ export const PREDICATE_CATALOG_4 = [
         argument_names: ["actor", "action", "resource", "decision"],
         argument_types: ["actor", "action", "resource", "decision"],
         ...closedArguments({ decision: DECISION_VOCABULARY }),
+        // One decision per actor, action and resource: an allow and a deny for
+        // the same three contradict (kb.pl builtin_decision_predicate/5).
+        key_arguments: ["actor", "action", "resource"],
         keywords: [
             "may",
             "can",
             "allowed",
+            "permitted",
             "denied",
             "forbidden",
             "must not",

package/dist/operations/modeling/predicate-loader.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"predicate-loader.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-loader.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,0CAA0C,CAAC;AAK3E,OAAO,KAAK,EACV,wBAAwB,EACxB,mBAAmB,EACpB,MAAM,sBAAsB,CAAC;AAI9B,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAExE;AAGD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,wBAAwB,GAAG,IAAI,CACxE,wBAAwB,EACxB,UAAU,CACX,GAAG;IACF,WAAW,EAAE,mBAAmB,CAAC;CAClC,CA4BA;AAGD,wBAAsB,4BAA4B,CAChD,MAAM,EAAE,UAAU,GAAG,IAAI,EACzB,sBAAsB,EAAE,OAAO,EAC/B,QAAQ,EAAE,MAAM,EAAE,GACjB,OAAO,CAAC,wBAAwB,EAAE,CAAC,CAwBrC;AAGD,wBAAgB,yBAAyB,CACvC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,wBAAwB,EAAE,CAwD5B;AAGD,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,mBAAmB,GAAG,SAAS,CAOjC;AAGD,wBAAgB,WAAW,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,EAAE,CAQpD"}
+{"version":3,"file":"predicate-loader.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-loader.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,0CAA0C,CAAC;AAK3E,OAAO,KAAK,EACV,wBAAwB,EACxB,mBAAmB,EACpB,MAAM,sBAAsB,CAAC;AAI9B,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAExE;AAGD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,wBAAwB,GAAG,IAAI,CACxE,wBAAwB,EACxB,UAAU,CACX,GAAG;IACF,WAAW,EAAE,mBAAmB,CAAC;CAClC,CA6BA;AAGD,wBAAsB,4BAA4B,CAChD,MAAM,EAAE,UAAU,GAAG,IAAI,EACzB,sBAAsB,EAAE,OAAO,EAC/B,QAAQ,EAAE,MAAM,EAAE,GACjB,OAAO,CAAC,wBAAwB,EAAE,CAAC,CAwBrC;AAGD,wBAAgB,yBAAyB,CACvC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,wBAAwB,EAAE,CA0D5B;AAGD,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,mBAAmB,GAAG,SAAS,CAOjC;AAGD,wBAAgB,WAAW,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,EAAE,CAQpD"}

package/dist/operations/modeling/predicate-loader.js

@@ -23,6 +23,7 @@ export function schemaForCandidate(schema) {
         ...(schema.argument_aliases
             ? { argument_aliases: schema.argument_aliases }
             : {}),
+        ...(schema.key_arguments ? { key_arguments: schema.key_arguments } : {}),
         ...(schema.aliases ? { aliases: schema.aliases } : {}),
         ...(schema.paraphrase_templates
             ? { paraphrase_templates: schema.paraphrase_templates }
@@ -64,6 +65,7 @@ export function predicateSchemaFromEntity(entity) {
         return [];
     const usageHints = usageHintsFromEntity(entity);
     const argumentDescriptions = stringArray(entity.argument_descriptions);
+    const keyArguments = stringArray(entity.key_arguments);
     const vocabulary = predicateVocabularyFromEntity(entity);
     return [
         {
@@ -93,6 +95,7 @@ export function predicateSchemaFromEntity(entity) {
                     ])),
                 }
                 : {}),
+            ...(keyArguments.length > 0 ? { key_arguments: keyArguments } : {}),
             keywords: [
                 predicateName,
                 ...stringArray(entity.aliases),

package/dist/operations/modeling/predicate-score-3.js

@@ -51,7 +51,7 @@ export function scoreExactPredicates3(schema, text) {
         return 0;
     }
     if (schema.predicate_name === "permission_rule") {
-        if (/^(?:only\s+)?[a-z][a-z\s_-]*\s+(?:may|can|is\s+allowed\s+to|must\s+not|cannot|can't|is\s+forbidden\s+to)\s+.+?\.?$/i.test(text)) {
+        if (/^(?:only\s+)?[a-z][a-z\s_-]*\s+(?:may|can|(?:is|are)\s+(?:not\s+)?(?:allowed|permitted|forbidden)\s+to|must\s+not|cannot|can't)\s+.+?\.?$/i.test(text)) {
             return 0.98;
         }
         return 0;

package/dist/operations/modeling/predicate-types.d.ts

@@ -16,6 +16,11 @@ export interface PredicateSchemaCandidate {
     argument_constants?: Record<string, string[]>;
     /** Legacy spellings keyed by argument name, each mapped to a constant. */
     argument_aliases?: Record<string, Record<string, string>>;
+    /**
+     * Argument names that determine the remaining arguments (a functional
+     * dependency). Two facts that agree on them describe the same case.
+     */
+    key_arguments?: string[];
     keywords: string[];
     /** Human-language aliases and controlled paraphrase templates used for deterministic retrieval. */
     aliases?: string[];

package/dist/operations/modeling/predicate-types.d.ts.map

@@ -1 +1 @@
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package/dist/operations/modeling/predicate-utils.d.ts.map

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package/dist/operations/modeling/predicate-utils.js

@@ -1,4 +1,5 @@
 import { createHash } from "node:crypto";
+import { singularizeToken } from "../semantic-advisor/shared.js";
 const DEFAULT_MIN_SCORE = 0.35;
 // implements REQ-mcp-suggest-predicates
 export function normalizeText(text) {
@@ -114,9 +115,7 @@ export function normalizePredicateToken(value) {
 }
 // implements REQ-mcp-suggest-predicates
 export function singularize(value) {
-    if (["changes", "status", "results"].includes(value))
-        return value;
-    return value.endsWith("s") && value.length > 3 ? value.slice(0, -1) : value;
+    return singularizeToken(value, ["changes", "status", "results"]);
 }
 // implements REQ-mcp-suggest-predicates
 export function normalizeSubjectKey(value) {