kibi-cli 0.2.3 → 0.2.5

package/dist/cli.js

@@ -15,33 +15,7 @@
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
-/*
- How to apply this header to source files (examples)
-
- 1) Prepend header to a single file (POSIX shells):
-
-    cat LICENSE_HEADER.txt "$FILE" > "$FILE".with-header && mv "$FILE".with-header "$FILE"
-
- 2) Apply to multiple files (example: the project's main entry files):
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp packages/cli/src/*.ts packages/mcp/src/*.ts; do
-      if [ -f "$f" ]; then
-        cp "$f" "$f".bak
-        (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-      fi
-    done
-
- 3) Avoid duplicating the header: run a quick guard to only add if missing
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp; do
-      if [ -f "$f" ]; then
-        if ! head -n 5 "$f" | grep -q "Copyright (C) 2026 Piotr Franczyk"; then
-          cp "$f" "$f".bak
-          (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-        fi
-      fi
-    done
-*/
+import { readFileSync } from "node:fs";
 import { Command } from "commander";
 import { branchEnsureCommand } from "./commands/branch.js";
 import { checkCommand } from "./commands/check.js";
@@ -50,7 +24,8 @@ import { gcCommand } from "./commands/gc.js";
 import { initCommand } from "./commands/init.js";
 import { queryCommand } from "./commands/query.js";
 import { syncCommand } from "./commands/sync.js";
-const VERSION = "0.1.0";
+const packageJson = JSON.parse(readFileSync(new URL("../package.json", import.meta.url), "utf8"));
+const VERSION = packageJson.version ?? "0.1.0";
 const program = new Command();
 program
     .name("kibi")

package/dist/commands/aggregated-checks.d.ts

@@ -4,6 +4,9 @@ import type { Violation } from "./check.js";
  * Run all checks using the aggregated Prolog predicates.
  * This makes a single Prolog call and parses JSON output, significantly
  * faster than running individual checks with multiple round-trips.
+ * @param prolog - The Prolog process
+ * @param rulesAllowlist - Set of rule names to run (null = all)
+ * @param requireAdr - Whether to require ADR constraints for symbol-traceability
  */
-export declare function runAggregatedChecks(prolog: PrologProcess, rulesAllowlist: Set<string> | null): Promise<Violation[]>;
+export declare function runAggregatedChecks(prolog: PrologProcess, rulesAllowlist: Set<string> | null, requireAdr?: boolean): Promise<Violation[]>;
 //# sourceMappingURL=aggregated-checks.d.ts.map

package/dist/commands/aggregated-checks.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"aggregated-checks.d.ts","sourceRoot":"","sources":["../../src/commands/aggregated-checks.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,aAAa,EAAmB,MAAM,cAAc,CAAC;AACnE,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAU5C;;;;GAIG;AACH,wBAAsB,mBAAmB,CACvC,MAAM,EAAE,aAAa,EACrB,cAAc,EAAE,GAAG,CAAC,MAAM,CAAC,GAAG,IAAI,GACjC,OAAO,CAAC,SAAS,EAAE,CAAC,CAqDtB"}
+{"version":3,"file":"aggregated-checks.d.ts","sourceRoot":"","sources":["../../src/commands/aggregated-checks.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,aAAa,EAAmB,MAAM,cAAc,CAAC;AAEnE,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAU5C;;;;;;;GAOG;AACH,wBAAsB,mBAAmB,CACvC,MAAM,EAAE,aAAa,EACrB,cAAc,EAAE,GAAG,CAAC,MAAM,CAAC,GAAG,IAAI,EAClC,UAAU,UAAQ,GACjB,OAAO,CAAC,SAAS,EAAE,CAAC,CA2DtB"}

package/dist/commands/aggregated-checks.js

@@ -1,15 +1,25 @@
 import path from "node:path";
 import { resolveKbPlPath } from "../prolog.js";
+import { escapeAtom } from "../prolog/codec.js";
 /**
  * Run all checks using the aggregated Prolog predicates.
  * This makes a single Prolog call and parses JSON output, significantly
  * faster than running individual checks with multiple round-trips.
+ * @param prolog - The Prolog process
+ * @param rulesAllowlist - Set of rule names to run (null = all)
+ * @param requireAdr - Whether to require ADR constraints for symbol-traceability
  */
-export async function runAggregatedChecks(prolog, rulesAllowlist) {
+export async function runAggregatedChecks(prolog, rulesAllowlist, requireAdr = false) {
     const violations = [];
     const checksPlPath = path.join(path.dirname(resolveKbPlPath()), "checks.pl");
-    const checksPlPathEscaped = checksPlPath.replace(/'/g, "''");
-    const query = `(use_module('${checksPlPathEscaped}'), call(checks:check_all_json(JsonString)))`;
+    const checksPlPathEscaped = escapeAtom(checksPlPath);
+    // Use check_all_json_with_options if available, otherwise fall back to check_all_json
+    const requireAdrStr = requireAdr ? "true" : "false";
+    const query = `(use_module('${checksPlPathEscaped}'), 
+    (   predicate_property(checks:check_all_json_with_options(_, _), _)
+    ->  call(checks:check_all_json_with_options(JsonString, ${requireAdrStr}))
+    ;   call(checks:check_all_json(JsonString))
+    ))`;
     try {
         const result = await prolog.query(query);
         if (!result.success) {

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

@@ -1 +1 @@
-{"version":3,"file":"branch.d.ts","sourceRoot":"","sources":["../../src/commands/branch.ts"],"names":[],"mappings":"AAwDA,MAAM,WAAW,mBAAmB;IAClC,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AA+DD,wBAAsB,mBAAmB,CACvC,OAAO,CAAC,EAAE,mBAAmB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAsBf;AAED,eAAe,mBAAmB,CAAC"}
+{"version":3,"file":"branch.d.ts","sourceRoot":"","sources":["../../src/commands/branch.ts"],"names":[],"mappings":"AA2BA,MAAM,WAAW,mBAAmB;IAClC,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAmDD,wBAAsB,mBAAmB,CACvC,OAAO,CAAC,EAAE,mBAAmB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAsBf;AAED,eAAe,mBAAmB,CAAC"}

package/dist/commands/branch.js

@@ -15,37 +15,9 @@
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
-/*
- How to apply this header to source files (examples)
-
- 1) Prepend header to a single file (POSIX shells):
-
-    cat LICENSE_HEADER.txt "$FILE" > "$FILE".with-header && mv "$FILE".with-header "$FILE"
-
- 2) Apply to multiple files (example: the project's main entry files):
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp packages/cli/src/*.ts packages/mcp/src/*.ts; do
-      if [ -f "$f" ]; then
-        cp "$f" "$f".bak
-        (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-      fi
-    done
-
- 3) Avoid duplicating the header: run a quick guard to only add if missing
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp; do
-      if [ -f "$f" ]; then
-        if ! head -n 5 "$f" | grep -q "Copyright (C) 2026 Piotr Franczyk"; then
-          cp "$f" "$f".bak
-          (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-        fi
-      fi
-    done
-*/
 import * as fs from "node:fs";
 import * as path from "node:path";
-import { copyCleanSnapshot, getBranchDiagnostic, isValidBranchName, resolveActiveBranch, resolveDefaultBranch, } from "../utils/branch-resolver.js";
-import { loadConfig } from "../utils/config.js";
+import { copyCleanSnapshot, getBranchDiagnostic, isValidBranchName, resolveActiveBranch, } from "../utils/branch-resolver.js";
 function resolveExplicitFromBranch(fromBranch) {
     if (!isValidBranchName(fromBranch)) {
         console.warn(`Warning: invalid branch name provided via --from: '${fromBranch}'`);
@@ -59,18 +31,8 @@ function resolveExplicitFromBranch(fromBranch) {
     return null;
 }
 function resolveDefaultSourceBranch() {
-    const config = loadConfig(process.cwd());
-    const defaultResult = resolveDefaultBranch(process.cwd(), config);
-    if ("branch" in defaultResult) {
-        const defaultBranch = defaultResult.branch;
-        const defaultPath = path.join(process.cwd(), ".kb/branches", defaultBranch);
-        if (fs.existsSync(defaultPath)) {
-            return defaultBranch;
-        }
-    }
-    else {
-        console.warn(`Warning: could not resolve default branch: ${defaultResult.error}`);
-    }
+    // No default branch concept - branches are independent
+    // When --from is not specified, an empty branch KB will be created
     return null;
 }
 function determineSourceBranch(explicitFromBranch) {

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

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AA+DA,MAAM,WAAW,YAAY;IAC3B,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CA2OvE"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AA2CA,MAAM,WAAW,YAAY;IAC3B,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CAuPvE"}

package/dist/commands/check.js

@@ -15,40 +15,16 @@
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
-/*
- How to apply this header to source files (examples)
-
- 1) Prepend header to a single file (POSIX shells):
-
-    cat LICENSE_HEADER.txt "$FILE" > "$FILE".with-header && mv "$FILE".with-header "$FILE"
-
- 2) Apply to multiple files (example: the project's main entry files):
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp packages/cli/src/*.ts packages/mcp/src/*.ts; do
-      if [ -f "$f" ]; then
-        cp "$f" "$f".bak
-        (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-      fi
-    done
-
- 3) Avoid duplicating the header: run a quick guard to only add if missing
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp; do
-      if [ -f "$f" ]; then
-        if ! head -n 5 "$f" | grep -q "Copyright (C) 2026 Piotr Franczyk"; then
-          cp "$f" "$f".bak
-          (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-        fi
-      fi
-    done
-*/
 import * as path from "node:path";
 import { PrologProcess } from "../prolog.js";
+import { escapeAtom } from "../prolog/codec.js";
 import { getStagedFiles } from "../traceability/git-staged.js";
 import { validateStagedMarkdown } from "../traceability/markdown-validate.js";
 import { extractSymbolsFromStagedFile } from "../traceability/symbol-extract.js";
 import { cleanupTempKb, consultOverlay, createOverlayFacts, createTempKb, } from "../traceability/temp-kb.js";
 import { formatViolations as formatStagedViolations, validateStagedSymbols, } from "../traceability/validate.js";
+import { loadConfig } from "../utils/config.js";
+import { RULES, getEffectiveRules, } from "../utils/rule-registry.js";
 import { runAggregatedChecks } from "./aggregated-checks.js";
 import { getCurrentBranch } from "./init-helpers.js";
 export async function checkCommand(options) {
@@ -111,7 +87,7 @@ export async function checkCommand(options) {
                 for (const f of codeFiles) {
                     try {
                         const symbols = extractSymbolsFromStagedFile(f);
-                        if (symbols && symbols.length) {
+                        if (symbols?.length) {
                             allSymbols.push(...symbols);
                         }
                     }
@@ -165,7 +141,7 @@ export async function checkCommand(options) {
         }
         const prolog = new PrologProcess({ timeout: 120000 });
         await prolog.start();
-        const kbPathEscaped = resolvedKbPath.replace(/'/g, "''");
+        const kbPathEscaped = escapeAtom(resolvedKbPath);
         const attachResult = await prolog.query(`kb_attach('${kbPathEscaped}')`);
         if (!attachResult.success) {
             await prolog.terminate();
@@ -173,21 +149,20 @@ export async function checkCommand(options) {
             process.exit(1);
         }
         const violations = [];
-        // Parse rules allowlist if provided
-        let rulesAllowlist = null;
-        if (options.rules) {
-            const parts = options.rules
-                .split(",")
-                .map((s) => s.trim())
-                .filter(Boolean);
-            rulesAllowlist = new Set(parts);
-        }
+        // Load config to get rule enablement settings
+        const config = loadConfig(process.cwd());
+        const checksConfig = config.checks ?? {
+            rules: Object.fromEntries(RULES.map((r) => [r.name, true])),
+            symbolTraceability: { requireAdr: false },
+        };
+        // Get effective rules based on config and CLI --rules filter
+        const effectiveRules = getEffectiveRules(checksConfig.rules, options.rules);
         // Helper to conditionally run a check by name
         async function runCheck(name, fn, ...args) {
-            if (rulesAllowlist?.has(name) === false)
+            if (!effectiveRules.has(name))
                 return;
             const res = await fn(prolog, ...args);
-            if (res && res.length)
+            if (res?.length)
                 violations.push(...res);
         }
         // Use aggregated checks (single Prolog call) when possible for better performance
@@ -196,27 +171,32 @@ export async function checkCommand(options) {
         const supportedRules = [
             "must-priority-coverage",
             "symbol-coverage",
+            "symbol-traceability",
             "no-dangling-refs",
             "no-cycles",
             "required-fields",
             "deprecated-adr-no-successor",
             "domain-contradictions",
         ];
-        const canUseAggregated = !rulesAllowlist ||
-            Array.from(rulesAllowlist).every((r) => supportedRules.includes(r));
+        const canUseAggregated = Array.from(effectiveRules).every((r) => supportedRules.includes(r));
         if (canUseAggregated) {
             // Fast path: single Prolog call returning all violations
-            const aggregatedViolations = await runAggregatedChecks(prolog, rulesAllowlist);
+            // Pass the requireAdr option for symbol-traceability
+            const aggregatedViolations = await runAggregatedChecks(prolog, effectiveRules, checksConfig.symbolTraceability?.requireAdr ?? false);
             violations.push(...aggregatedViolations);
         }
         else {
             // Legacy path: individual checks for backward compatibility
             await runCheck("must-priority-coverage", checkMustPriorityCoverage);
             await runCheck("symbol-coverage", checkSymbolCoverage);
+            await runCheck("symbol-traceability", (p) => checkSymbolTraceability(p, checksConfig.symbolTraceability?.requireAdr ?? false));
             await runCheck("no-dangling-refs", checkNoDanglingRefs);
             await runCheck("no-cycles", checkNoCycles);
             const allEntityIds = await getAllEntityIds(prolog);
-            await runCheck("required-fields", checkRequiredFields, allEntityIds);
+            if (effectiveRules.has("required-fields")) {
+                const requiredViolations = await checkRequiredFields(prolog, allEntityIds);
+                violations.push(...requiredViolations);
+            }
             await runCheck("deprecated-adr-no-successor", checkDeprecatedAdrs);
             await runCheck("domain-contradictions", checkDomainContradictions);
         }
@@ -573,6 +553,36 @@ async function checkSymbolCoverage(prolog) {
     }
     return violations;
 }
+async function checkSymbolTraceability(prolog, requireAdr) {
+    const violations = [];
+    const requireAdrStr = requireAdr ? "true" : "false";
+    const result = await prolog.query(`findall(violation(Rule, EntityId, Desc, Sugg, Src), 
+      checks:symbol_traceability_violation(${requireAdrStr}, violation(Rule, EntityId, Desc, Sugg, Src)), 
+      Violations)`);
+    if (!result.success || !result.bindings.Violations) {
+        return violations;
+    }
+    // Parse the violations from Prolog format
+    const violationsStr = result.bindings.Violations;
+    if (violationsStr && violationsStr !== "[]") {
+        // Parse each violation term
+        const violationRegex = /violation\(([^,]+),'?([^',]+)'?,([^,]+),([^,]+),'?([^']*)'?\)/g;
+        let match;
+        do {
+            match = violationRegex.exec(violationsStr);
+            if (match) {
+                violations.push({
+                    rule: match[1].trim().replace(/^'|'$/g, ""),
+                    entityId: match[2].trim(),
+                    description: match[3].trim().replace(/^"|"$/g, ""),
+                    suggestion: match[4].trim().replace(/^"|"$/g, ""),
+                    source: match[5].trim() || undefined,
+                });
+            }
+        } while (match);
+    }
+    return violations;
+}
 function parseTripleRows(raw) {
     const cleaned = raw.trim();
     if (cleaned === "[]" || cleaned.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":"AAsDA,wBAAsB,aAAa,IAAI,OAAO,CAAC,IAAI,CAAC,CA0DnD"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AA2BA,wBAAsB,aAAa,IAAI,OAAO,CAAC,IAAI,CAAC,CA0DnD"}

package/dist/commands/doctor.js

@@ -15,33 +15,6 @@
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
-/*
- How to apply this header to source files (examples)
-
- 1) Prepend header to a single file (POSIX shells):
-
-    cat LICENSE_HEADER.txt "$FILE" > "$FILE".with-header && mv "$FILE".with-header "$FILE"
-
- 2) Apply to multiple files (example: the project's main entry files):
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp packages/cli/src/*.ts packages/mcp/src/*.ts; do
-      if [ -f "$f" ]; then
-        cp "$f" "$f".bak
-        (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-      fi
-    done
-
- 3) Avoid duplicating the header: run a quick guard to only add if missing
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp; do
-      if [ -f "$f" ]; then
-        if ! head -n 5 "$f" | grep -q "Copyright (C) 2026 Piotr Franczyk"; then
-          cp "$f" "$f".bak
-          (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-        fi
-      fi
-    done
-*/
 import { execSync } from "node:child_process";
 import { existsSync, readFileSync, statSync } from "node:fs";
 import * as path from "node:path";

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

@@ -1 +1 @@
-{"version":3,"file":"gc.d.ts","sourceRoot":"","sources":["../../src/commands/gc.ts"],"names":[],"mappings":"AAmDA,wBAAsB,SAAS,CAAC,OAAO,EAAE;IACvC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,iBAsGA;AAED,eAAe,SAAS,CAAC"}
+{"version":3,"file":"gc.d.ts","sourceRoot":"","sources":["../../src/commands/gc.ts"],"names":[],"mappings":"AAsBA,wBAAsB,SAAS,CAAC,OAAO,EAAE;IACvC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,iBAiFA;AAED,eAAe,SAAS,CAAC"}

package/dist/commands/gc.js

@@ -15,38 +15,9 @@
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
-/*
- How to apply this header to source files (examples)
-
- 1) Prepend header to a single file (POSIX shells):
-
-    cat LICENSE_HEADER.txt "$FILE" > "$FILE".with-header && mv "$FILE".with-header "$FILE"
-
- 2) Apply to multiple files (example: the project's main entry files):
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp packages/cli/src/*.ts packages/mcp/src/*.ts; do
-      if [ -f "$f" ]; then
-        cp "$f" "$f".bak
-        (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-      fi
-    done
-
- 3) Avoid duplicating the header: run a quick guard to only add if missing
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp; do
-      if [ -f "$f" ]; then
-        if ! head -n 5 "$f" | grep -q "Copyright (C) 2026 Piotr Franczyk"; then
-          cp "$f" "$f".bak
-          (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-        fi
-      fi
-    done
-*/
 import { execSync } from "node:child_process";
 import * as fs from "node:fs";
 import * as path from "node:path";
-import { resolveDefaultBranch } from "../utils/branch-resolver.js";
-import { loadConfig } from "../utils/config.js";
 export async function gcCommand(options) {
     // If force is true, perform deletion. Otherwise default to dry run.
     const dryRun = options?.force ? false : (options?.dryRun ?? true);
@@ -87,28 +58,8 @@ export async function gcCommand(options) {
             .readdirSync(kbRoot, { withFileTypes: true })
             .filter((d) => d.isDirectory())
             .map((d) => d.name);
-        // Resolve configured/default branch to protect
-        const config = loadConfig(process.cwd());
-        // Prefer explicit configured defaultBranch if set
-        const configured = config?.defaultBranch;
-        let defaultBranch;
-        if (configured && typeof configured === "string" && configured.trim()) {
-            defaultBranch = configured.trim();
-        }
-        else {
-            const resolved = resolveDefaultBranch(process.cwd(), config);
-            defaultBranch =
-                "branch" in resolved && typeof resolved.branch === "string"
-                    ? resolved.branch
-                    : "main";
-        }
-        // Protect resolved branch and its 'master'->'main' normalization
-        const protectedBranches = new Set([defaultBranch]);
-        if (defaultBranch === "main")
-            protectedBranches.add("master");
-        if (defaultBranch === "master")
-            protectedBranches.add("main");
-        const staleBranches = kbBranches.filter((kb) => !protectedBranches.has(kb) && !gitBranches.has(kb));
+        // Branches are protected if they exist in git - no default branch concept
+        const staleBranches = kbBranches.filter((kb) => !gitBranches.has(kb));
         // Perform deletion when dryRun is false (force requested)
         const performDelete = !dryRun;
         let deletedCount = 0;

package/dist/commands/init-helpers.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init-helpers.d.ts","sourceRoot":"","sources":["../../src/commands/init-helpers.ts"],"names":[],"mappings":"AA8GA,wBAAsB,gBAAgB,CACpC,GAAG,GAAE,MAAsB,GAC1B,OAAO,CAAC,MAAM,CAAC,CASjB;AAED,wBAAgB,0BAA0B,CACxC,KAAK,EAAE,MAAM,EACb,aAAa,EAAE,MAAM,GACpB,IAAI,CAQN;AAED,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAMpD;AAED,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAajD;AAED,wBAAsB,eAAe,CACnC,KAAK,EAAE,MAAM,EACb,eAAe,EAAE,MAAM,GACtB,OAAO,CAAC,IAAI,CAAC,CAYf;AAED,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAuBnE;AAED,wBAAgB,eAAe,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAiBpD"}
+{"version":3,"file":"init-helpers.d.ts","sourceRoot":"","sources":["../../src/commands/init-helpers.ts"],"names":[],"mappings":"AAmFA,wBAAsB,gBAAgB,CACpC,GAAG,GAAE,MAAsB,GAC1B,OAAO,CAAC,MAAM,CAAC,CASjB;AAED,wBAAgB,0BAA0B,CACxC,KAAK,EAAE,MAAM,EACb,aAAa,EAAE,MAAM,GACpB,IAAI,CAQN;AAED,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAMpD;AAED,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAajD;AAED,wBAAsB,eAAe,CACnC,KAAK,EAAE,MAAM,EACb,eAAe,EAAE,MAAM,GACtB,OAAO,CAAC,IAAI,CAAC,CAYf;AASD,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAmCnE;AAED,wBAAgB,eAAe,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAiBpD"}

package/dist/commands/init-helpers.js

@@ -15,33 +15,6 @@
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
-/*
- How to apply this header to source files (examples)
-
- 1) Prepend header to a single file (POSIX shells):
-
-    cat LICENSE_HEADER.txt "$FILE" > "$FILE".with-header && mv "$FILE".with-header "$FILE"
-
- 2) Apply to multiple files (example: the project's main entry files):
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp packages/cli/src/*.ts packages/mcp/src/*.ts; do
-      if [ -f "$f" ]; then
-        cp "$f" "$f".bak
-        (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-      fi
-    done
-
- 3) Avoid duplicating the header: run a quick guard to only add if missing
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp; do
-      if [ -f "$f" ]; then
-        if ! head -n 5 "$f" | grep -q "Copyright (C) 2026 Piotr Franczyk"; then
-          cp "$f" "$f".bak
-          (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-        fi
-      fi
-    done
-*/
 import { chmodSync, copyFileSync, existsSync, mkdirSync, readFileSync, writeFileSync, } from "node:fs";
 import * as path from "node:path";
 import fg from "fast-glob";
@@ -58,7 +31,7 @@ branch_flag=$3
 
 if [ "$branch_flag" = "1" ]; then
   # Try to resolve the branch we just left (strip decorations like ^ and ~)
-  old_branch=$(git name-rev --name-only "$old_ref" 2>/dev/null | sed 's/\^.*//')
+  old_branch=$(git name-rev --name-only "$old_ref" 2>/dev/null | sed 's/\\^.*//')
 
   # Basic validation: non-empty and does not contain ~ or ^
   if [ -n "$old_branch" ] && echo "$old_branch" | grep -qv '[~^]'; then
@@ -138,21 +111,35 @@ export async function copySchemaFiles(kbDir, schemaSourceDir) {
     }
     console.log(`✓ Copied ${schemaFiles.length} schema files`);
 }
+const KIBI_HOOK_BEGIN = "# BEGIN kibi-managed";
+const KIBI_HOOK_END = "# END kibi-managed";
+function escapeRegex(s) {
+    return s.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+}
 export function installHook(hookPath, content) {
+    const kibiSection = `${KIBI_HOOK_BEGIN}\n${content}\n${KIBI_HOOK_END}`;
     if (existsSync(hookPath)) {
         const existing = readFileSync(hookPath, "utf8");
-        if (!existing.includes("kibi")) {
-            writeFileSync(hookPath, `${existing}
-${content}`, {
-                mode: 0o755,
-            });
+        if (existing.includes(KIBI_HOOK_BEGIN) &&
+            existing.includes(KIBI_HOOK_END)) {
+            // Replace only the kibi-managed section, preserving any user-authored content
+            const updated = existing.replace(new RegExp(`${escapeRegex(KIBI_HOOK_BEGIN)}[\\s\\S]*?${escapeRegex(KIBI_HOOK_END)}`), kibiSection);
+            writeFileSync(hookPath, updated, { mode: 0o755 });
+        }
+        else if (existing.includes("kibi branch ensure")) {
+            // Legacy format: already has the complete kibi logic, skip
+            return;
+        }
+        else {
+            // Hook exists with user content (no kibi section) - append kibi section
+            const shebang = existing.startsWith("#!/") ? "" : "#!/bin/sh\n";
+            writeFileSync(hookPath, `${shebang}${existing.trimEnd()}\n${kibiSection}\n`, { mode: 0o755 });
         }
     }
     else {
-        writeFileSync(hookPath, `#!/bin/sh
-${content}`, { mode: 0o755 });
+        writeFileSync(hookPath, `#!/bin/sh\n${kibiSection}\n`, { mode: 0o755 });
     }
-    // Explicitly ensure hook is executable (mode option can be inconsistent in Docker)
+    // Explicitly ensure hook is executable
     chmodSync(hookPath, 0o755);
 }
 export function installGitHooks(gitDir) {

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

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AA4DA,UAAU,WAAW;IACnB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA6DrE"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AAiCA,UAAU,WAAW;IACnB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA6DrE"}

package/dist/commands/init.js

@@ -15,33 +15,6 @@
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
-/*
- How to apply this header to source files (examples)
-
- 1) Prepend header to a single file (POSIX shells):
-
-    cat LICENSE_HEADER.txt "$FILE" > "$FILE".with-header && mv "$FILE".with-header "$FILE"
-
- 2) Apply to multiple files (example: the project's main entry files):
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp packages/cli/src/*.ts packages/mcp/src/*.ts; do
-      if [ -f "$f" ]; then
-        cp "$f" "$f".bak
-        (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-      fi
-    done
-
- 3) Avoid duplicating the header: run a quick guard to only add if missing
-
-    for f in packages/cli/bin/kibi packages/mcp/bin/kibi-mcp; do
-      if [ -f "$f" ]; then
-        if ! head -n 5 "$f" | grep -q "Copyright (C) 2026 Piotr Franczyk"; then
-          cp "$f" "$f".bak
-          (cat LICENSE_HEADER.txt; echo; cat "$f" ) > "$f".new && mv "$f".new "$f"
-        fi
-      fi
-    done
-*/
 import { existsSync } from "node:fs";
 import * as path from "node:path";
 import { fileURLToPath } from "node:url";

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

@@ -1 +1 @@
-{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../src/commands/query.ts"],"names":[],"mappings":"AAqDA,UAAU,YAAY;IACpB,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC1B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAsB,YAAY,CAChC,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,OAAO,EAAE,YAAY,GACpB,OAAO,CAAC,IAAI,CAAC,CAmLf"}
+{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../src/commands/query.ts"],"names":[],"mappings":"AAmCA,UAAU,YAAY;IACpB,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC1B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAsB,YAAY,CAChC,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,OAAO,EAAE,YAAY,GACpB,OAAO,CAAC,IAAI,CAAC,CAyKf"}