@monoes/monograph 1.1.0 → 1.2.0

package/dist/src/__tests__/analysis/file-classifier.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"file-classifier.test.js","sourceRoot":"","sources":["../../../../src/__tests__/analysis/file-classifier.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,mCAAmC,CAAC;AAElF,QAAQ,CAAC,cAAc,EAAE,GAAG,EAAE;IAC5B,EAAE,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACvC,MAAM,CAAC,YAAY,CAAC,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAClD,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,2BAA2B,EAAE,GAAG,EAAE;QACnC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAC/C,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,iCAAiC,EAAE,GAAG,EAAE;QACzC,MAAM,CAAC,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACpC,MAAM,CAAC,YAAY,CAAC,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IACtD,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,yBAAyB,EAAE,GAAG,EAAE;QACjC,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACjD,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,yBAAyB,EAAE,GAAG,EAAE;QACjC,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACjD,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACvC,MAAM,CAAC,YAAY,CAAC,kCAAkC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,oCAAoC,EAAE,GAAG,EAAE;QAC5C,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAChD,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,mCAAmC,EAAE,GAAG,EAAE;QAC3C,MAAM,CAAC,YAAY,CAAC,+BAA+B,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACtE,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,QAAQ,CAAC,yBAAyB,EAAE,GAAG,EAAE;IACvC,EAAE,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACpC,MAAM,CAAC,eAAe,CAAC,mCAAmC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IAC7E,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACpC,MAAM,CAAC,eAAe,CAAC,kCAAkC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IAC5E,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC7B,MAAM,CAAC,eAAe,CAAC,6BAA6B,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACvE,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,0BAA0B,EAAE,GAAG,EAAE;QAClC,MAAM,CAAC,eAAe,CAAC,uCAAuC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACjF,CAAC,CAAC,CAAC;IACH,EAAE,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAChD,MAAM,CAAC,eAAe,CAAC,+BAA+B,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IAC7E,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/dist/src/__tests__/analysis/node-similarity.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=node-similarity.test.d.ts.map

package/dist/src/__tests__/analysis/node-similarity.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"node-similarity.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/analysis/node-similarity.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/analysis/node-similarity.test.js

@@ -0,0 +1,66 @@
+import { describe, it, expect } from 'vitest';
+import { jaccardSimilarity, findSimilarNodes, buildNeighborMap, } from '../../analysis/node-similarity.js';
+describe('jaccardSimilarity', () => {
+    it('returns 1 for identical sets', () => {
+        expect(jaccardSimilarity(new Set(['a', 'b', 'c']), new Set(['a', 'b', 'c']))).toBeCloseTo(1);
+    });
+    it('returns 0 for disjoint sets', () => {
+        expect(jaccardSimilarity(new Set(['a', 'b']), new Set(['c', 'd']))).toBeCloseTo(0);
+    });
+    it('returns 1/3 for sets with one shared and two unique elements', () => {
+        // intersection={b}, union={a,b,c} => 1/3
+        expect(jaccardSimilarity(new Set(['a', 'b']), new Set(['b', 'c']))).toBeCloseTo(1 / 3);
+    });
+    it('returns 0 for two empty sets', () => {
+        expect(jaccardSimilarity(new Set(), new Set())).toBeCloseTo(0);
+    });
+    it('returns 0 when one set is empty and other is not', () => {
+        expect(jaccardSimilarity(new Set(['a']), new Set())).toBeCloseTo(0);
+    });
+});
+describe('buildNeighborMap', () => {
+    it('builds an undirected adjacency map', () => {
+        const edges = [
+            { sourceId: 'a', targetId: 'b' },
+            { sourceId: 'b', targetId: 'c' },
+        ];
+        const map = buildNeighborMap(edges);
+        expect(map.get('a')).toEqual(new Set(['b']));
+        expect(map.get('b')).toEqual(new Set(['a', 'c']));
+        expect(map.get('c')).toEqual(new Set(['b']));
+    });
+});
+describe('findSimilarNodes', () => {
+    const edges = [
+        { sourceId: 'a', targetId: 'b' },
+        { sourceId: 'a', targetId: 'c' },
+        { sourceId: 'a', targetId: 'd' },
+        { sourceId: 'x', targetId: 'b' },
+        { sourceId: 'x', targetId: 'c' },
+        { sourceId: 'x', targetId: 'd' },
+        { sourceId: 'y', targetId: 'e' },
+    ];
+    it('returns nodes sorted by jaccard similarity descending', () => {
+        const results = findSimilarNodes('a', edges, 5);
+        // 'x' shares all 3 neighbors (b,c,d) — should be top result
+        expect(results[0]?.nodeId).toBe('x');
+        expect(results[0]?.score).toBeGreaterThan(0.5);
+    });
+    it('respects the k limit', () => {
+        const results = findSimilarNodes('a', edges, 1);
+        expect(results.length).toBe(1);
+    });
+    it('excludes the query node itself', () => {
+        const results = findSimilarNodes('a', edges, 10);
+        expect(results.every(r => r.nodeId !== 'a')).toBe(true);
+    });
+    it('returns empty array for unknown node', () => {
+        const results = findSimilarNodes('unknown', edges, 5);
+        expect(results).toHaveLength(0);
+    });
+    it('returns only nodes with score > 0', () => {
+        const results = findSimilarNodes('a', edges, 10);
+        expect(results.every(r => r.score > 0)).toBe(true);
+    });
+});
+//# sourceMappingURL=node-similarity.test.js.map

package/dist/src/__tests__/analysis/node-similarity.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"node-similarity.test.js","sourceRoot":"","sources":["../../../../src/__tests__/analysis/node-similarity.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EACL,iBAAiB,EACjB,gBAAgB,EAChB,gBAAgB,GACjB,MAAM,mCAAmC,CAAC;AAE3C,QAAQ,CAAC,mBAAmB,EAAE,GAAG,EAAE;IACjC,EAAE,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACtC,MAAM,CAAC,iBAAiB,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,EAAE,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;IAC/F,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACrC,MAAM,CAAC,iBAAiB,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,EAAE,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;IACrF,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,8DAA8D,EAAE,GAAG,EAAE;QACtE,yCAAyC;QACzC,MAAM,CAAC,iBAAiB,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,EAAE,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;IACzF,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACtC,MAAM,CAAC,iBAAiB,CAAC,IAAI,GAAG,EAAE,EAAE,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;IACjE,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,kDAAkD,EAAE,GAAG,EAAE;QAC1D,MAAM,CAAC,iBAAiB,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;IACtE,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,QAAQ,CAAC,kBAAkB,EAAE,GAAG,EAAE;IAChC,EAAE,CAAC,oCAAoC,EAAE,GAAG,EAAE;QAC5C,MAAM,KAAK,GAAG;YACZ,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;YAChC,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;SACjC,CAAC;QACF,MAAM,GAAG,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAC;QACpC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QAC7C,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC;QAClD,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,QAAQ,CAAC,kBAAkB,EAAE,GAAG,EAAE;IAChC,MAAM,KAAK,GAAG;QACZ,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;QAChC,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;QAChC,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;QAChC,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;QAChC,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;QAChC,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;QAChC,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,EAAE;KACjC,CAAC;IAEF,EAAE,CAAC,uDAAuD,EAAE,GAAG,EAAE;QAC/D,MAAM,OAAO,GAAG,gBAAgB,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC;QAChD,4DAA4D;QAC5D,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QACrC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC;IACjD,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAC9B,MAAM,OAAO,GAAG,gBAAgB,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC;QAChD,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IACjC,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,gCAAgC,EAAE,GAAG,EAAE;QACxC,MAAM,OAAO,GAAG,gBAAgB,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC;QACjD,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC1D,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAC9C,MAAM,OAAO,GAAG,gBAAgB,CAAC,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC;QACtD,MAAM,CAAC,OAAO,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;IAClC,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,mCAAmC,EAAE,GAAG,EAAE;QAC3C,MAAM,OAAO,GAAG,gBAAgB,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC;QACjD,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/dist/src/__tests__/cache/augment-cache.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=augment-cache.test.d.ts.map

package/dist/src/__tests__/cache/augment-cache.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"augment-cache.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/cache/augment-cache.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/cache/augment-cache.test.js

@@ -0,0 +1,47 @@
+import { describe, it, expect, beforeEach } from 'vitest';
+import { createAugmentCache } from '../../cache/augment-cache.js';
+describe('AugmentCache', () => {
+    let cache;
+    beforeEach(() => {
+        cache = createAugmentCache({ maxSize: 3, ttlMs: 60_000 });
+    });
+    it('stores and retrieves a value by key', () => {
+        cache.set('k1', 'result1');
+        expect(cache.get('k1')).toBe('result1');
+    });
+    it('returns undefined for a missing key', () => {
+        expect(cache.get('missing')).toBeUndefined();
+    });
+    it('evicts the oldest entry when maxSize is exceeded', () => {
+        cache.set('k1', 'v1');
+        cache.set('k2', 'v2');
+        cache.set('k3', 'v3');
+        cache.set('k4', 'v4');
+        expect(cache.get('k1')).toBeUndefined();
+        expect(cache.get('k4')).toBe('v4');
+    });
+    it('expires entries after TTL', async () => {
+        const shortCache = createAugmentCache({ maxSize: 10, ttlMs: 10 });
+        shortCache.set('k1', 'v1');
+        await new Promise(r => setTimeout(r, 20));
+        expect(shortCache.get('k1')).toBeUndefined();
+    });
+    it('reports size correctly', () => {
+        cache.set('k1', 'v1');
+        cache.set('k2', 'v2');
+        expect(cache.size()).toBe(2);
+    });
+    it('clears all entries', () => {
+        cache.set('k1', 'v1');
+        cache.set('k2', 'v2');
+        cache.clear();
+        expect(cache.size()).toBe(0);
+    });
+    it('provides a makeKey helper that encodes all relevant params', () => {
+        const { makeKey } = cache;
+        const k = makeKey('query', '/repo', 10, 'markdown');
+        expect(k).toContain('query');
+        expect(k).toContain('/repo');
+    });
+});
+//# sourceMappingURL=augment-cache.test.js.map

package/dist/src/__tests__/cache/augment-cache.test.js.map

@@ -0,0 +1 @@
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package/dist/src/__tests__/cli/check-update.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=check-update.test.d.ts.map

package/dist/src/__tests__/cli/check-update.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"check-update.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/cli/check-update.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/cli/check-update.test.js

@@ -0,0 +1,38 @@
+import { describe, it, expect } from 'vitest';
+import Database from 'better-sqlite3';
+import { checkUpdate } from '../../cli/check-update.js';
+function makeDb(indexedAt = null) {
+    const db = new Database(':memory:');
+    db.exec(`
+    CREATE TABLE index_meta (key TEXT PRIMARY KEY, value TEXT);
+  `);
+    if (indexedAt) {
+        db.prepare("INSERT INTO index_meta VALUES ('indexed_at', ?)").run(indexedAt);
+    }
+    return db;
+}
+describe('checkUpdate', () => {
+    it('returns needsUpdate=true when index is very old', () => {
+        const db = makeDb('2020-01-01T00:00:00.000Z');
+        const result = checkUpdate(db, { maxAgeMs: 1000 });
+        expect(result.needsUpdate).toBe(true);
+    });
+    it('returns needsUpdate=false when index is fresh', () => {
+        const db = makeDb(new Date().toISOString());
+        const result = checkUpdate(db, { maxAgeMs: 60_000 });
+        expect(result.needsUpdate).toBe(false);
+    });
+    it('returns needsUpdate=true when index_meta has no indexed_at', () => {
+        const db = makeDb(null);
+        const result = checkUpdate(db, {});
+        expect(result.needsUpdate).toBe(true);
+    });
+    it('returns indexedAt and ageMs in result', () => {
+        const now = new Date().toISOString();
+        const db = makeDb(now);
+        const result = checkUpdate(db, { maxAgeMs: 60_000 });
+        expect(result.indexedAt).toBe(now);
+        expect(typeof result.ageMs).toBe('number');
+    });
+});
+//# sourceMappingURL=check-update.test.js.map

package/dist/src/__tests__/cli/check-update.test.js.map

@@ -0,0 +1 @@
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package/dist/src/__tests__/cli/hooks-install.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=hooks-install.test.d.ts.map

package/dist/src/__tests__/cli/hooks-install.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"hooks-install.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/cli/hooks-install.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/cli/hooks-install.test.js

@@ -0,0 +1,48 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtempSync, rmSync, mkdirSync, readFileSync, existsSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { installGitHooks, uninstallGitHooks, listInstalledHooks } from '../../cli/hooks-install.js';
+describe('installGitHooks', () => {
+    let tmpDir;
+    let hooksDir;
+    beforeEach(() => {
+        tmpDir = mkdtempSync(join(tmpdir(), 'hooks-test-'));
+        hooksDir = join(tmpDir, '.git', 'hooks');
+        mkdirSync(hooksDir, { recursive: true });
+    });
+    afterEach(() => {
+        rmSync(tmpDir, { recursive: true, force: true });
+    });
+    it('creates pre-commit hook with monograph build command', () => {
+        installGitHooks(tmpDir, ['pre-commit']);
+        const hookPath = join(hooksDir, 'pre-commit');
+        expect(existsSync(hookPath)).toBe(true);
+        const content = readFileSync(hookPath, 'utf8');
+        expect(content).toContain('monograph');
+        expect(content).toContain('#!/');
+    });
+    it('creates post-merge hook', () => {
+        installGitHooks(tmpDir, ['post-merge']);
+        expect(existsSync(join(hooksDir, 'post-merge'))).toBe(true);
+    });
+    it('creates both hooks when both specified', () => {
+        installGitHooks(tmpDir, ['pre-commit', 'post-merge']);
+        expect(existsSync(join(hooksDir, 'pre-commit'))).toBe(true);
+        expect(existsSync(join(hooksDir, 'post-merge'))).toBe(true);
+    });
+    it('throws when .git directory does not exist', () => {
+        expect(() => installGitHooks('/nonexistent/repo', ['pre-commit'])).toThrow();
+    });
+    it('lists installed hooks', () => {
+        installGitHooks(tmpDir, ['pre-commit']);
+        const installed = listInstalledHooks(tmpDir);
+        expect(installed).toContain('pre-commit');
+    });
+    it('uninstalls a hook', () => {
+        installGitHooks(tmpDir, ['pre-commit']);
+        uninstallGitHooks(tmpDir, ['pre-commit']);
+        expect(existsSync(join(hooksDir, 'pre-commit'))).toBe(false);
+    });
+});
+//# sourceMappingURL=hooks-install.test.js.map

package/dist/src/__tests__/cli/hooks-install.test.js.map

@@ -0,0 +1 @@
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package/dist/src/__tests__/cli/hooks-marker.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=hooks-marker.test.d.ts.map

package/dist/src/__tests__/cli/hooks-marker.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"hooks-marker.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/cli/hooks-marker.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/cli/hooks-marker.test.js

@@ -0,0 +1,115 @@
+/**
+ * Tests for marker-based hook management enhancements.
+ * Covers: append-not-overwrite, uninstall-only-marker-block, post-checkout,
+ * Husky detection, rebase guards, and per-hook status details.
+ */
+import { describe, it, expect, afterEach } from 'vitest';
+import { mkdtempSync, rmSync, mkdirSync, writeFileSync, readFileSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { installGitHooks, uninstallGitHooks, getHookStatus, HOOK_MARKER_START, } from '../../cli/hooks-install.js';
+function makeRepo() {
+    const dir = mkdtempSync(join(tmpdir(), 'mhook-'));
+    mkdirSync(join(dir, '.git', 'hooks'), { recursive: true });
+    return dir;
+}
+describe('marker-based append (not overwrite)', () => {
+    let tmpDir;
+    afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
+    it('appends monograph block to existing hook content', () => {
+        tmpDir = makeRepo();
+        const hookPath = join(tmpDir, '.git', 'hooks', 'pre-commit');
+        const existing = '#!/bin/sh\necho "my custom hook"\n';
+        writeFileSync(hookPath, existing, 'utf8');
+        installGitHooks(tmpDir, ['pre-commit']);
+        const content = readFileSync(hookPath, 'utf8');
+        expect(content).toContain('my custom hook'); // existing preserved
+        expect(content).toContain(HOOK_MARKER_START);
+        expect(content).toContain('monograph');
+    });
+    it('does not duplicate the block on repeated installs', () => {
+        tmpDir = makeRepo();
+        installGitHooks(tmpDir, ['pre-commit']);
+        installGitHooks(tmpDir, ['pre-commit']);
+        const content = readFileSync(join(tmpDir, '.git', 'hooks', 'pre-commit'), 'utf8');
+        const count = (content.match(new RegExp(HOOK_MARKER_START, 'g')) ?? []).length;
+        expect(count).toBe(1);
+    });
+});
+describe('marker-based uninstall (only removes block)', () => {
+    let tmpDir;
+    afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
+    it('removes only the monograph block, leaves rest of hook intact', () => {
+        tmpDir = makeRepo();
+        const hookPath = join(tmpDir, '.git', 'hooks', 'pre-commit');
+        writeFileSync(hookPath, '#!/bin/sh\necho "keep this"\n', 'utf8');
+        installGitHooks(tmpDir, ['pre-commit']);
+        uninstallGitHooks(tmpDir, ['pre-commit']);
+        const content = readFileSync(hookPath, 'utf8');
+        expect(content).toContain('keep this');
+        expect(content).not.toContain(HOOK_MARKER_START);
+        expect(content).not.toContain('monograph build');
+    });
+    it('deletes the file if it was created entirely by monograph (no prior content)', () => {
+        tmpDir = makeRepo();
+        installGitHooks(tmpDir, ['pre-commit']);
+        uninstallGitHooks(tmpDir, ['pre-commit']);
+        // file should no longer contain the marker block
+        const hookPath = join(tmpDir, '.git', 'hooks', 'pre-commit');
+        try {
+            const content = readFileSync(hookPath, 'utf8');
+            expect(content).not.toContain(HOOK_MARKER_START);
+        }
+        catch {
+            // file deleted entirely is also acceptable
+        }
+    });
+});
+describe('post-checkout hook support', () => {
+    let tmpDir;
+    afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
+    it('installs post-checkout hook', () => {
+        tmpDir = makeRepo();
+        installGitHooks(tmpDir, ['post-checkout']);
+        const content = readFileSync(join(tmpDir, '.git', 'hooks', 'post-checkout'), 'utf8');
+        expect(content).toContain('monograph');
+    });
+    it('post-checkout hook includes rebase/merge skip guard', () => {
+        tmpDir = makeRepo();
+        installGitHooks(tmpDir, ['post-checkout']);
+        const content = readFileSync(join(tmpDir, '.git', 'hooks', 'post-checkout'), 'utf8');
+        // Should skip during rebase or merge operations
+        expect(content).toMatch(/rebase|MERGE|cherry-pick/i);
+    });
+});
+describe('rebase guard in hook scripts', () => {
+    let tmpDir;
+    afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
+    it('pre-commit hook includes rebase skip guard', () => {
+        tmpDir = makeRepo();
+        installGitHooks(tmpDir, ['pre-commit']);
+        const content = readFileSync(join(tmpDir, '.git', 'hooks', 'pre-commit'), 'utf8');
+        expect(content).toMatch(/rebase|MERGE|cherry-pick/i);
+    });
+});
+describe('per-hook status (getHookStatus with details)', () => {
+    let tmpDir;
+    afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
+    it('returns per-hook detail objects', () => {
+        tmpDir = makeRepo();
+        installGitHooks(tmpDir, ['pre-commit', 'post-checkout']);
+        const status = getHookStatus(tmpDir);
+        expect(status.perHook).toBeDefined();
+        const preCommit = status.perHook['pre-commit'];
+        expect(preCommit).toBeDefined();
+        expect(preCommit.installed).toBe(true);
+    });
+    it('perHook shows not-installed for hooks that were not set up', () => {
+        tmpDir = makeRepo();
+        installGitHooks(tmpDir, ['pre-commit']);
+        const status = getHookStatus(tmpDir);
+        const postMerge = status.perHook?.['post-merge'];
+        expect(postMerge?.installed ?? false).toBe(false);
+    });
+});
+//# sourceMappingURL=hooks-marker.test.js.map

package/dist/src/__tests__/cli/hooks-marker.test.js.map

@@ -0,0 +1 @@
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package/dist/src/__tests__/cli/hooks-status.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=hooks-status.test.d.ts.map

package/dist/src/__tests__/cli/hooks-status.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"hooks-status.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/cli/hooks-status.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/cli/hooks-status.test.js

@@ -0,0 +1,36 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtempSync, rmSync, mkdirSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { installGitHooks, getHookStatus } from '../../cli/hooks-install.js';
+describe('getHookStatus', () => {
+    let tmpDir;
+    beforeEach(() => {
+        tmpDir = mkdtempSync(join(tmpdir(), 'hook-status-'));
+        mkdirSync(join(tmpDir, '.git', 'hooks'), { recursive: true });
+    });
+    afterEach(() => { rmSync(tmpDir, { recursive: true, force: true }); });
+    it('returns installed=false when no hooks present', () => {
+        const status = getHookStatus(tmpDir);
+        expect(status.installed).toBe(false);
+        expect(status.hooks).toEqual([]);
+    });
+    it('returns installed=true when hooks are present', () => {
+        installGitHooks(tmpDir, ['pre-commit', 'post-merge']);
+        const status = getHookStatus(tmpDir);
+        expect(status.installed).toBe(true);
+        expect(status.hooks).toContain('pre-commit');
+        expect(status.hooks).toContain('post-merge');
+    });
+    it('returns hooksDir path', () => {
+        const status = getHookStatus(tmpDir);
+        expect(status.hooksDir).toContain('.git/hooks');
+    });
+    it('returns installed=false when .git dir missing', () => {
+        const noGitDir = mkdtempSync(join(tmpdir(), 'no-git-'));
+        const status = getHookStatus(noGitDir);
+        expect(status.installed).toBe(false);
+        rmSync(noGitDir, { recursive: true, force: true });
+    });
+});
+//# sourceMappingURL=hooks-status.test.js.map

package/dist/src/__tests__/cli/hooks-status.test.js.map

@@ -0,0 +1 @@
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package/dist/src/__tests__/export/adjacency-matrix.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=adjacency-matrix.test.d.ts.map

package/dist/src/__tests__/export/adjacency-matrix.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"adjacency-matrix.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/export/adjacency-matrix.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/export/adjacency-matrix.test.js

@@ -0,0 +1,103 @@
+import { describe, it, expect } from 'vitest';
+import { buildAdjacencyMatrix, buildAdjacencyMatrixFromDb, adjacencyMatrixToCsv, } from '../../export/adjacency-matrix.js';
+import { openDb } from '../../storage/db.js';
+import { join } from 'path';
+import { mkdtempSync } from 'fs';
+import { tmpdir } from 'os';
+function makeTempDb() {
+    const dir = mkdtempSync(join(tmpdir(), 'monograph-adjmatrix-test-'));
+    return openDb(join(dir, 'test.db'));
+}
+function insertNode(db, id) {
+    db.prepare(`INSERT INTO nodes (id, label, name, norm_label, is_exported) VALUES (?, 'Function', ?, ?, 0)`)
+        .run(id, id, id.toLowerCase());
+}
+function insertEdge(db, src, tgt) {
+    db.prepare(`INSERT INTO edges (id, source_id, target_id, relation, confidence, confidence_score) VALUES (?, ?, ?, 'CALLS', 'EXTRACTED', 1.0)`)
+        .run(`${src}_${tgt}`, src, tgt);
+}
+function makeNode(id) {
+    return { id, label: 'Function', name: id, normLabel: id.toLowerCase(), isExported: false };
+}
+function makeEdge(src, tgt) {
+    return { id: `${src}_${tgt}`, sourceId: src, targetId: tgt, relation: 'CALLS', confidence: 'EXTRACTED', confidenceScore: 1.0 };
+}
+describe('buildAdjacencyMatrix', () => {
+    it('builds a zero matrix for no edges', () => {
+        const nodes = [makeNode('a'), makeNode('b')];
+        const result = buildAdjacencyMatrix(nodes, []);
+        expect(result.nodeIds).toEqual(['a', 'b']);
+        expect(result.matrix[0]).toEqual([0, 0]);
+        expect(result.matrix[1]).toEqual([0, 0]);
+    });
+    it('counts a single edge correctly', () => {
+        const nodes = [makeNode('a'), makeNode('b'), makeNode('c')];
+        const edges = [makeEdge('a', 'b')];
+        const result = buildAdjacencyMatrix(nodes, edges);
+        // a→b: matrix[0][1] = 1, all others = 0
+        expect(result.matrix[0][1]).toBe(1);
+        expect(result.matrix[0][0]).toBe(0);
+        expect(result.matrix[1][0]).toBe(0);
+    });
+    it('counts multi-edges between the same pair', () => {
+        const nodes = [makeNode('a'), makeNode('b')];
+        const e1 = { ...makeEdge('a', 'b'), id: 'e1' };
+        const e2 = { ...makeEdge('a', 'b'), id: 'e2' };
+        const result = buildAdjacencyMatrix(nodes, [e1, e2]);
+        expect(result.matrix[0][1]).toBe(2);
+    });
+    it('ignores edges whose endpoints are not in the node list', () => {
+        const nodes = [makeNode('a'), makeNode('b')];
+        const dangling = makeEdge('a', 'z'); // 'z' not in nodes
+        const result = buildAdjacencyMatrix(nodes, [dangling]);
+        expect(result.matrix[0][0]).toBe(0);
+        expect(result.matrix[0][1]).toBe(0);
+    });
+});
+describe('buildAdjacencyMatrixFromDb', () => {
+    it('builds matrix from all nodes in db', () => {
+        const db = makeTempDb();
+        insertNode(db, 'a');
+        insertNode(db, 'b');
+        insertNode(db, 'c');
+        insertEdge(db, 'a', 'b');
+        insertEdge(db, 'b', 'c');
+        const result = buildAdjacencyMatrixFromDb(db);
+        expect(result.nodeIds).toHaveLength(3);
+        // Find indices
+        const ai = result.nodeIds.indexOf('a');
+        const bi = result.nodeIds.indexOf('b');
+        expect(result.matrix[ai][bi]).toBe(1);
+        db.close();
+    });
+    it('restricts to given nodeIds subset', () => {
+        const db = makeTempDb();
+        insertNode(db, 'a');
+        insertNode(db, 'b');
+        insertNode(db, 'c');
+        insertEdge(db, 'a', 'b');
+        const result = buildAdjacencyMatrixFromDb(db, ['a', 'b']);
+        expect(result.nodeIds).toHaveLength(2);
+        expect(result.nodeIds).not.toContain('c');
+        db.close();
+    });
+});
+describe('adjacencyMatrixToCsv', () => {
+    it('generates a CSV with node names as headers', () => {
+        const am = buildAdjacencyMatrix([makeNode('a'), makeNode('b')], [makeEdge('a', 'b')]);
+        const csv = adjacencyMatrixToCsv(am);
+        const lines = csv.split('\n');
+        expect(lines[0]).toContain('"a"');
+        expect(lines[0]).toContain('"b"');
+        // Row for 'a': first cell is "a", second is 1
+        const aRow = lines.find(l => l.startsWith('"a"'));
+        expect(aRow).toContain('1');
+    });
+    it('escapes double quotes in node names', () => {
+        const node = { id: 'x', label: 'Function', name: 'say "hello"', normLabel: 'say hello', isExported: false };
+        const am = buildAdjacencyMatrix([node], []);
+        const csv = adjacencyMatrixToCsv(am);
+        expect(csv).toContain('""hello""');
+    });
+});
+//# sourceMappingURL=adjacency-matrix.test.js.map

package/dist/src/__tests__/export/adjacency-matrix.test.js.map

@@ -0,0 +1 @@
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package/dist/src/__tests__/export/csv.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=csv.test.d.ts.map

package/dist/src/__tests__/export/csv.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"csv.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/export/csv.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/export/csv.test.js

@@ -0,0 +1,34 @@
+import { describe, it, expect } from 'vitest';
+import { toCsv } from '../../export/csv.js';
+const node = {
+    id: 'n1', label: 'Function', name: 'doStuff',
+    normLabel: 'function', filePath: '/a.ts',
+    startLine: 1, endLine: 5, isExported: true,
+};
+const edge = {
+    id: 'e1', sourceId: 'n1', targetId: 'n2',
+    relation: 'CALLS', confidence: 'EXTRACTED', confidenceScore: 0.9,
+};
+describe('toCsv', () => {
+    it('emits node CSV header and row', () => {
+        const { nodes } = toCsv([node], []);
+        expect(nodes).toContain('id,label,name,filePath,isExported,startLine,endLine');
+        expect(nodes).toContain('n1,Function,doStuff,/a.ts,true,1,5');
+    });
+    it('emits edge CSV header and row', () => {
+        const { edges } = toCsv([node], [edge]);
+        expect(edges).toContain('id,sourceId,targetId,relation,confidence,confidenceScore');
+        expect(edges).toContain('e1,n1,n2,CALLS,EXTRACTED,0.9');
+    });
+    it('escapes commas in names', () => {
+        const n = { ...node, name: 'foo,bar' };
+        const { nodes } = toCsv([n], []);
+        expect(nodes).toContain('"foo,bar"');
+    });
+    it('returns two separate CSV strings', () => {
+        const result = toCsv([node], [edge]);
+        expect(typeof result.nodes).toBe('string');
+        expect(typeof result.edges).toBe('string');
+    });
+});
+//# sourceMappingURL=csv.test.js.map