refactor(phase5): remove Graphology dependency, delete src/graphs/

- Uninstall graphology and graphology-types from package.json
- Move attachment-types.ts → src/lib/attachment-types.ts
- Move code-types.ts → src/lib/parsers/code-types.ts
- Move file-lang.ts → src/lib/file-lang.ts
- Move manager-types.ts → src/lib/embed-types.ts (only EmbedFn/EmbedFns remain)
- Delete file-index-types.ts (unused)
- Delete src/graphs/ directory entirely
- Update all imports to new locations

1407 tests pass. Zero Graphology references remain.

Author: prih

package-lock.json

@@ -61,7 +61,6 @@
     "dotenv": "^17.3.1",
     "express": "^5.2.1",
     "express-rate-limit": "^8.3.1",
-    "graphology": "^0.26.0",
     "jsonwebtoken": "^9.0.3",
     "micromatch": "^4.0.8",
     "mime": "^4.1.0",
@@ -88,7 +87,6 @@
     "@types/node": "^25.4.0",
     "@types/supertest": "^7.2.0",
     "@types/ws": "^8.18.1",
-    "graphology-types": "^0.24.8",
     "jest": "^30.3.0",
     "supertest": "^7.2.2",
     "ts-jest": "^29.4.6",

package.json

@@ -85,7 +85,7 @@ import * as recallSkills from '@/api/tools/skills/recall-skills';
 import * as bumpSkillUsage from '@/api/tools/skills/bump-usage';
 import * as getContext from '@/api/tools/context/get-context';
 
-import type { EmbedFn, EmbedFns } from '@/graphs/manager-types';
+import type { EmbedFn, EmbedFns } from '@/lib/embed-types';
 
 export type { EmbedFn, EmbedFns };
 

src/api/index.ts

@@ -7,7 +7,7 @@ import { parseCodeFile } from '@/lib/parsers/code';
 import { startWatcher, ALWAYS_IGNORED, type WatcherHandle } from '@/lib/watcher';
 import { INDEXER_PREVIEW_LEN } from '@/lib/defaults';
 import { normalizePathForEmbed } from '@/lib/path-utils';
-import { getLanguage, getMimeType } from '@/graphs/file-lang';
+import { getLanguage, getMimeType } from '@/lib/file-lang';
 import type { ProjectScopedStore, DocsStore, CodeStore, FilesStore, CodeNode } from '@/store/types';
 import { createLogger } from '@/lib/logger';
 

src/cli/indexer.ts

@@ -2,7 +2,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 import type { TaskStatus, TaskPriority } from '../store/types/tasks';
 import type { SkillSource } from '../store/types/skills';
-import type { AttachmentMeta } from '../graphs/attachment-types';
+import type { AttachmentMeta } from './attachment-types';
 import type { EpicStatus } from '../store/types/epics';
 import type { RelationFrontmatter } from './file-mirror';
 import type { ParsedNoteFile, ParsedTaskFile, ParsedSkillFile, ParsedEpicFile } from './file-import';

src/graphs/file-index-types.ts

@@ -4,9 +4,9 @@ import { parseMarkdown } from './frontmatter';
 import type { RelationFrontmatter } from './file-mirror';
 import type { TaskStatus, TaskPriority } from '../store/types/tasks';
 import type { SkillSource } from '../store/types/skills';
-import type { AttachmentMeta } from '../graphs/attachment-types';
+import type { AttachmentMeta } from './attachment-types';
 import type { EpicStatus } from '../store/types/epics';
-import { scanAttachments } from '../graphs/attachment-types';
+import { scanAttachments } from './attachment-types';
 import { readEvents, replayNoteEvents, replayTaskEvents, replaySkillEvents, replayEpicEvents } from './events-log';
 import { createLogger } from '@/lib/logger';