@rbalchii/anchor-engine 4.7.0

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Files changed (539) hide show
  1. package/LICENSE +609 -0
  2. package/README.md +317 -0
  3. package/anchor.bat +5 -0
  4. package/docs/API.md +314 -0
  5. package/docs/DEPLOYMENT.md +448 -0
  6. package/docs/INDEX.md +226 -0
  7. package/docs/STAR_Whitepaper_Executive.md +216 -0
  8. package/docs/TROUBLESHOOTING.md +535 -0
  9. package/docs/archive/GIT_BACKUP_VERIFICATION.md +297 -0
  10. package/docs/archive/adoption-guide.md +264 -0
  11. package/docs/archive/adoption-preparation.md +179 -0
  12. package/docs/archive/agent-harness-integration.md +227 -0
  13. package/docs/archive/api-reference.md +106 -0
  14. package/docs/archive/api_flows_diagram.md +118 -0
  15. package/docs/archive/architecture.md +410 -0
  16. package/docs/archive/architecture_diagram.md +174 -0
  17. package/docs/archive/broader-adoption-preparation.md +175 -0
  18. package/docs/archive/browser-paradigm-architecture.md +163 -0
  19. package/docs/archive/chat-integration.md +124 -0
  20. package/docs/archive/community-adoption-materials.md +103 -0
  21. package/docs/archive/community-adoption.md +147 -0
  22. package/docs/archive/comparison-with-siloed-solutions.md +192 -0
  23. package/docs/archive/comprehensive-docs.md +156 -0
  24. package/docs/archive/data_flow_diagram.md +251 -0
  25. package/docs/archive/enhancement-implementation-summary.md +146 -0
  26. package/docs/archive/evolution-summary.md +141 -0
  27. package/docs/archive/ingestion_pipeline_diagram.md +198 -0
  28. package/docs/archive/native-module-profiling-results.md +135 -0
  29. package/docs/archive/positioning-document.md +158 -0
  30. package/docs/archive/positioning.md +175 -0
  31. package/docs/archive/query-builder-documentation.md +218 -0
  32. package/docs/archive/quick-reference.md +40 -0
  33. package/docs/archive/quickstart.md +63 -0
  34. package/docs/archive/relationship-narrative-discovery.md +141 -0
  35. package/docs/archive/search-logic-improvement-plan.md +336 -0
  36. package/docs/archive/search_architecture_diagram.md +212 -0
  37. package/docs/archive/semantic-architecture-guide.md +97 -0
  38. package/docs/archive/sequence-diagrams.md +128 -0
  39. package/docs/archive/system_components_diagram.md +296 -0
  40. package/docs/archive/test-framework-integration.md +109 -0
  41. package/docs/archive/testing-framework-documentation.md +397 -0
  42. package/docs/archive/testing-framework-summary.md +121 -0
  43. package/docs/archive/testing-framework.md +377 -0
  44. package/docs/archive/ui-architecture.md +75 -0
  45. package/docs/arxiv/BIBLIOGRAPHY.bib +145 -0
  46. package/docs/arxiv/RELATED_WORK.tex +39 -0
  47. package/docs/arxiv/compile.bat +48 -0
  48. package/docs/arxiv/joss_response.md +33 -0
  49. package/docs/arxiv/prepare-submission.bat +46 -0
  50. package/docs/arxiv/review.md +128 -0
  51. package/docs/arxiv/star-whitepaper.tex +657 -0
  52. package/docs/code-patterns.md +289 -0
  53. package/docs/whitepaper.md +445 -0
  54. package/engine/dist/agent/runtime.d.ts +41 -0
  55. package/engine/dist/agent/runtime.d.ts.map +1 -0
  56. package/engine/dist/agent/runtime.js +73 -0
  57. package/engine/dist/agent/runtime.js.map +1 -0
  58. package/engine/dist/commands/audit-tags.d.ts +14 -0
  59. package/engine/dist/commands/audit-tags.d.ts.map +1 -0
  60. package/engine/dist/commands/audit-tags.js +180 -0
  61. package/engine/dist/commands/audit-tags.js.map +1 -0
  62. package/engine/dist/commands/distill.d.ts +19 -0
  63. package/engine/dist/commands/distill.d.ts.map +1 -0
  64. package/engine/dist/commands/distill.js +114 -0
  65. package/engine/dist/commands/distill.js.map +1 -0
  66. package/engine/dist/commands/generate-synonyms.d.ts +14 -0
  67. package/engine/dist/commands/generate-synonyms.d.ts.map +1 -0
  68. package/engine/dist/commands/generate-synonyms.js +91 -0
  69. package/engine/dist/commands/generate-synonyms.js.map +1 -0
  70. package/engine/dist/config/index.d.ts +115 -0
  71. package/engine/dist/config/index.d.ts.map +1 -0
  72. package/engine/dist/config/index.js +326 -0
  73. package/engine/dist/config/index.js.map +1 -0
  74. package/engine/dist/config/max-recall-config.d.ts +102 -0
  75. package/engine/dist/config/max-recall-config.d.ts.map +1 -0
  76. package/engine/dist/config/max-recall-config.js +102 -0
  77. package/engine/dist/config/max-recall-config.js.map +1 -0
  78. package/engine/dist/config/paths.d.ts +40 -0
  79. package/engine/dist/config/paths.d.ts.map +1 -0
  80. package/engine/dist/config/paths.js +49 -0
  81. package/engine/dist/config/paths.js.map +1 -0
  82. package/engine/dist/core/batch.d.ts +19 -0
  83. package/engine/dist/core/batch.d.ts.map +1 -0
  84. package/engine/dist/core/batch.js +37 -0
  85. package/engine/dist/core/batch.js.map +1 -0
  86. package/engine/dist/core/db.d.ts +58 -0
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  88. package/engine/dist/core/db.js +563 -0
  89. package/engine/dist/core/db.js.map +1 -0
  90. package/engine/dist/core/inference/ChatWorker.d.ts +2 -0
  91. package/engine/dist/core/inference/ChatWorker.d.ts.map +1 -0
  92. package/engine/dist/core/inference/ChatWorker.js +28 -0
  93. package/engine/dist/core/inference/ChatWorker.js.map +1 -0
  94. package/engine/dist/core/inference/context_manager.d.ts +49 -0
  95. package/engine/dist/core/inference/context_manager.d.ts.map +1 -0
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  97. package/engine/dist/core/inference/context_manager.js.map +1 -0
  98. package/engine/dist/core/inference/llamaLoaderWorker.d.ts +2 -0
  99. package/engine/dist/core/inference/llamaLoaderWorker.d.ts.map +1 -0
  100. package/engine/dist/core/inference/llamaLoaderWorker.js +23 -0
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  102. package/engine/dist/core/vector.d.ts +40 -0
  103. package/engine/dist/core/vector.d.ts.map +1 -0
  104. package/engine/dist/core/vector.js +167 -0
  105. package/engine/dist/core/vector.js.map +1 -0
  106. package/engine/dist/index.d.ts +4 -0
  107. package/engine/dist/index.d.ts.map +1 -0
  108. package/engine/dist/index.js +400 -0
  109. package/engine/dist/index.js.map +1 -0
  110. package/engine/dist/middleware/auth.d.ts +14 -0
  111. package/engine/dist/middleware/auth.d.ts.map +1 -0
  112. package/engine/dist/middleware/auth.js +44 -0
  113. package/engine/dist/middleware/auth.js.map +1 -0
  114. package/engine/dist/middleware/request-tracing.d.ts +29 -0
  115. package/engine/dist/middleware/request-tracing.d.ts.map +1 -0
  116. package/engine/dist/middleware/request-tracing.js +115 -0
  117. package/engine/dist/middleware/request-tracing.js.map +1 -0
  118. package/engine/dist/middleware/validate.d.ts +30 -0
  119. package/engine/dist/middleware/validate.d.ts.map +1 -0
  120. package/engine/dist/middleware/validate.js +117 -0
  121. package/engine/dist/middleware/validate.js.map +1 -0
  122. package/engine/dist/native/index.d.ts +106 -0
  123. package/engine/dist/native/index.d.ts.map +1 -0
  124. package/engine/dist/native/index.js +230 -0
  125. package/engine/dist/native/index.js.map +1 -0
  126. package/engine/dist/native/types.d.ts +45 -0
  127. package/engine/dist/native/types.d.ts.map +1 -0
  128. package/engine/dist/native/types.js +6 -0
  129. package/engine/dist/native/types.js.map +1 -0
  130. package/engine/dist/profiling/atomization-profiling.d.ts +8 -0
  131. package/engine/dist/profiling/atomization-profiling.d.ts.map +1 -0
  132. package/engine/dist/profiling/atomization-profiling.js +108 -0
  133. package/engine/dist/profiling/atomization-profiling.js.map +1 -0
  134. package/engine/dist/profiling/bottleneck-identification.d.ts +8 -0
  135. package/engine/dist/profiling/bottleneck-identification.d.ts.map +1 -0
  136. package/engine/dist/profiling/bottleneck-identification.js +249 -0
  137. package/engine/dist/profiling/bottleneck-identification.js.map +1 -0
  138. package/engine/dist/profiling/content-sanitization-profiling.d.ts +12 -0
  139. package/engine/dist/profiling/content-sanitization-profiling.d.ts.map +1 -0
  140. package/engine/dist/profiling/content-sanitization-profiling.js +266 -0
  141. package/engine/dist/profiling/content-sanitization-profiling.js.map +1 -0
  142. package/engine/dist/profiling/simhash-profiling.d.ts +11 -0
  143. package/engine/dist/profiling/simhash-profiling.d.ts.map +1 -0
  144. package/engine/dist/profiling/simhash-profiling.js +168 -0
  145. package/engine/dist/profiling/simhash-profiling.js.map +1 -0
  146. package/engine/dist/routes/api.d.ts +9 -0
  147. package/engine/dist/routes/api.d.ts.map +1 -0
  148. package/engine/dist/routes/api.js +37 -0
  149. package/engine/dist/routes/api.js.map +1 -0
  150. package/engine/dist/routes/enhanced-api.d.ts +9 -0
  151. package/engine/dist/routes/enhanced-api.d.ts.map +1 -0
  152. package/engine/dist/routes/enhanced-api.js +139 -0
  153. package/engine/dist/routes/enhanced-api.js.map +1 -0
  154. package/engine/dist/routes/health.d.ts +8 -0
  155. package/engine/dist/routes/health.d.ts.map +1 -0
  156. package/engine/dist/routes/health.js +89 -0
  157. package/engine/dist/routes/health.js.map +1 -0
  158. package/engine/dist/routes/monitoring.d.ts +8 -0
  159. package/engine/dist/routes/monitoring.d.ts.map +1 -0
  160. package/engine/dist/routes/monitoring.js +509 -0
  161. package/engine/dist/routes/monitoring.js.map +1 -0
  162. package/engine/dist/routes/v1/admin.d.ts +3 -0
  163. package/engine/dist/routes/v1/admin.d.ts.map +1 -0
  164. package/engine/dist/routes/v1/admin.js +261 -0
  165. package/engine/dist/routes/v1/admin.js.map +1 -0
  166. package/engine/dist/routes/v1/atoms.d.ts +3 -0
  167. package/engine/dist/routes/v1/atoms.d.ts.map +1 -0
  168. package/engine/dist/routes/v1/atoms.js +172 -0
  169. package/engine/dist/routes/v1/atoms.js.map +1 -0
  170. package/engine/dist/routes/v1/backup.d.ts +3 -0
  171. package/engine/dist/routes/v1/backup.d.ts.map +1 -0
  172. package/engine/dist/routes/v1/backup.js +100 -0
  173. package/engine/dist/routes/v1/backup.js.map +1 -0
  174. package/engine/dist/routes/v1/git.d.ts +3 -0
  175. package/engine/dist/routes/v1/git.d.ts.map +1 -0
  176. package/engine/dist/routes/v1/git.js +316 -0
  177. package/engine/dist/routes/v1/git.js.map +1 -0
  178. package/engine/dist/routes/v1/ingest.d.ts +3 -0
  179. package/engine/dist/routes/v1/ingest.d.ts.map +1 -0
  180. package/engine/dist/routes/v1/ingest.js +66 -0
  181. package/engine/dist/routes/v1/ingest.js.map +1 -0
  182. package/engine/dist/routes/v1/memory.d.ts +14 -0
  183. package/engine/dist/routes/v1/memory.d.ts.map +1 -0
  184. package/engine/dist/routes/v1/memory.js +87 -0
  185. package/engine/dist/routes/v1/memory.js.map +1 -0
  186. package/engine/dist/routes/v1/research.d.ts +3 -0
  187. package/engine/dist/routes/v1/research.d.ts.map +1 -0
  188. package/engine/dist/routes/v1/research.js +109 -0
  189. package/engine/dist/routes/v1/research.js.map +1 -0
  190. package/engine/dist/routes/v1/search.d.ts +3 -0
  191. package/engine/dist/routes/v1/search.d.ts.map +1 -0
  192. package/engine/dist/routes/v1/search.js +180 -0
  193. package/engine/dist/routes/v1/search.js.map +1 -0
  194. package/engine/dist/routes/v1/settings.d.ts +8 -0
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  198. package/engine/dist/routes/v1/system.d.ts +3 -0
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  202. package/engine/dist/routes/v1/tags.d.ts +3 -0
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  206. package/engine/dist/server-8080.d.ts +2 -0
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  210. package/engine/dist/services/backup/backup-restore.d.ts +37 -0
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  218. package/engine/dist/services/distillation/radial-distiller-v2.d.ts +127 -0
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  226. package/engine/dist/services/health-check-enhanced.d.ts +89 -0
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  230. package/engine/dist/services/idle-manager.d.ts +56 -0
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  242. package/engine/dist/services/ingest/atomizer-service.d.ts +74 -0
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@@ -0,0 +1,289 @@
1
+ # Anchor Engine Code Patterns Guide
2
+
3
+ A tour of the programming patterns used throughout the codebase.
4
+
5
+ ## Overview
6
+
7
+ The Anchor Engine uses a **hybrid approach** - mixing functional and imperative patterns where each makes sense:
8
+
9
+ - **~31,000 lines** of TypeScript
10
+ - **125 files** across 12 modules
11
+ - **Functional** for data transformations
12
+ - **Imperative** for performance-critical loops
13
+ - **Async/await** for I/O operations
14
+
15
+ ---
16
+
17
+ ## 1. Functional Patterns
18
+
19
+ ### Pure Functions
20
+ Functions that don't mutate state and return predictable outputs.
21
+
22
+ **Example: `calculateLightweightScore` (search.ts)**
23
+ ```typescript
24
+ function calculateLightweightScore(
25
+ result: SearchResult,
26
+ queryTerms: string[],
27
+ query: string
28
+ ): number {
29
+ // Immutable operations only
30
+ const contentWords = new Set(content.split(/\s+/).filter(w => w.length > 2));
31
+
32
+ // No side effects - just calculations
33
+ return Math.min(1.0, baseScore * 0.3 + termScore * 0.5 + ...);
34
+ }
35
+ ```
36
+
37
+ **Used for:**
38
+ - Scoring algorithms
39
+ - Data transformations
40
+ - Configuration merging
41
+
42
+ ### Higher-Order Functions
43
+ Functions that take or return other functions.
44
+
45
+ **Example: `processWithAdaptiveConcurrency` (adaptive-concurrency.ts)**
46
+ ```typescript
47
+ export async function processWithAdaptiveConcurrency<T, R>(
48
+ items: T[],
49
+ processor: (item: T, index: number) => Promise<R>, // ← Function argument
50
+ config?: ConcurrencyConfig
51
+ ): Promise<R[]> {
52
+ // Abstracts the concurrency logic
53
+ const results = await processor(item, index);
54
+ }
55
+ ```
56
+
57
+ **Used for:**
58
+ - Abstracting processing patterns
59
+ - Middleware chains
60
+ - Batch operations
61
+
62
+ ### Array Methods (Map/Filter/Reduce)
63
+ Declarative data transformations.
64
+
65
+ **Example: Result processing (search.ts)**
66
+ ```typescript
67
+ const scoredAtoms = rawAtoms.map(atom => ({
68
+ ...atom,
69
+ score: calculateLightweightScore(atom, terms, sanitizedQuery)
70
+ }))
71
+ .sort((a, b) => (b.score || 0) - (a.score || 0))
72
+ .slice(0, maxResultsPerTerm * terms.length);
73
+ ```
74
+
75
+ **Used for:**
76
+ - Data pipelines
77
+ - Result formatting
78
+ - Scoring and ranking
79
+
80
+ ---
81
+
82
+ ## 2. Imperative Patterns
83
+
84
+ ### For Loops with Index
85
+ When you need precise control over iteration.
86
+
87
+ **Example: Range merging deduplication (search.ts)**
88
+ ```typescript
89
+ for (let i = 1; i < compoundAnchors.length; i++) {
90
+ const next = compoundAnchors[i];
91
+ const currentEnd = (current.end_byte || 0);
92
+ const nextStart = (next.start_byte || 0);
93
+
94
+ // Complex overlap logic requires mutable state
95
+ if (nextStart <= currentEnd + 50) {
96
+ // Merge or skip based on conditions
97
+ continue;
98
+ }
99
+ }
100
+ ```
101
+
102
+ **Used for:**
103
+ - Complex deduplication
104
+ - Sliding window algorithms
105
+ - Performance-critical paths
106
+
107
+ ### While Loops
108
+ For unknown iteration counts.
109
+
110
+ **Example: BFS traversal (explore.ts)**
111
+ ```typescript
112
+ for (let depth = 0; depth < maxDepth && frontier.length > 0; depth++) {
113
+ const nextFrontier: string[] = [];
114
+
115
+ for (const chunk of chunks) {
116
+ // Process current frontier
117
+ // Build nextFrontier for next iteration
118
+ }
119
+
120
+ frontier = nextFrontier; // ← State mutation
121
+ }
122
+ ```
123
+
124
+ **Used for:**
125
+ - Graph traversals
126
+ - Queue processing
127
+ - Streaming data
128
+
129
+ ### Mutable State
130
+ When performance matters more than purity.
131
+
132
+ **Example: Batch processing (context-inflator.ts)**
133
+ ```typescript
134
+ const results: R[] = [];
135
+
136
+ for (let i = 0; i < items.length; i += batchSize) {
137
+ const batch = items.slice(i, i + batchSize);
138
+ const batchResults = await Promise.all(
139
+ batch.map((item, batchIndex) => processor(item, i + batchIndex))
140
+ );
141
+ results.push(...batchResults); // ← Mutating results array
142
+ }
143
+ ```
144
+
145
+ **Used for:**
146
+ - Accumulating results
147
+ - Caching
148
+ - Performance optimization
149
+
150
+ ---
151
+
152
+ ## 3. Async/Await Patterns
153
+
154
+ ### Sequential Processing
155
+ One at a time - memory safe.
156
+
157
+ ```typescript
158
+ for (const item of items) {
159
+ const result = await processor(item);
160
+ results.push(result);
161
+ }
162
+ ```
163
+
164
+ **Used for:** Low-memory environments (mobile)
165
+
166
+ ### Parallel Processing with Promise.all
167
+ Batch concurrency for speed.
168
+
169
+ ```typescript
170
+ const batchPromises = batch.map((item, batchIndex) =>
171
+ processor(item, i + batchIndex)
172
+ );
173
+ const batchResults = await Promise.all(batchPromises);
174
+ ```
175
+
176
+ **Used for:** High-memory systems (desktops)
177
+
178
+ ### Error Handling with Try/Catch
179
+ Graceful degradation.
180
+
181
+ ```typescript
182
+ try {
183
+ const result = await db.run(query, params);
184
+ return result.rows;
185
+ } catch (e) {
186
+ console.error('[Search] Query failed:', e);
187
+ return []; // ← Graceful fallback
188
+ }
189
+ ```
190
+
191
+ **Used for:** Database queries, file I/O, external APIs
192
+
193
+ ---
194
+
195
+ ## 4. Object-Oriented Patterns
196
+
197
+ ### Static Methods
198
+ Utility functions grouped by domain.
199
+
200
+ **Example: ContextInflator (context-inflator.ts)**
201
+ ```typescript
202
+ export class ContextInflator {
203
+ static async inflate(results: SearchResult[], ...): Promise<SearchResult[]> {
204
+ // Implementation
205
+ }
206
+
207
+ static async inflateFromAtomPositions(...): Promise<SearchResult[]> {
208
+ // Implementation
209
+ }
210
+ }
211
+ ```
212
+
213
+ **Used for:** Namespacing utility functions
214
+
215
+ ### Interfaces for Type Safety
216
+ ```typescript
217
+ export interface ConcurrencyConfig {
218
+ forceSequential?: boolean;
219
+ sequentialThresholdMB?: number;
220
+ // ...
221
+ }
222
+ ```
223
+
224
+ **Used for:** Configuration objects, API contracts
225
+
226
+ ---
227
+
228
+ ## 5. Design Patterns
229
+
230
+ ### Strategy Pattern
231
+ Different algorithms based on conditions.
232
+
233
+ **Example: Adaptive concurrency**
234
+ ```typescript
235
+ if (concurrency === 1) {
236
+ // Sequential strategy
237
+ for (let i = 0; i < items.length; i++) { ... }
238
+ } else {
239
+ // Parallel strategy
240
+ for (let i = 0; i < items.length; i += batchSize) { ... }
241
+ }
242
+ ```
243
+
244
+ ### Memoization/Caching
245
+ ```typescript
246
+ let cachedSettings: any = null;
247
+ let settingsLastRead = 0;
248
+
249
+ function loadUserSettings(): any {
250
+ if (cachedSettings && (now - settingsLastRead) < SETTINGS_CACHE_MS) {
251
+ return cachedSettings; // ← Return cached
252
+ }
253
+ // ... load fresh
254
+ }
255
+ ```
256
+
257
+ ### Guard Clauses
258
+ Early returns for edge cases.
259
+ ```typescript
260
+ if (!result.content) return result.score || 0;
261
+ if (terms.length === 0) return [];
262
+ if (!databaseReady) throw new Error('Not ready');
263
+ ```
264
+
265
+ ---
266
+
267
+ ## Pattern Selection Guide
268
+
269
+ | Pattern | Use When | Example |
270
+ |---------|----------|---------|
271
+ | **Pure Function** | Data transformation, scoring | `calculateLightweightScore` |
272
+ | **Higher-Order** | Abstract processing logic | `processWithAdaptiveConcurrency` |
273
+ | **For Loop** | Complex iteration logic | Range merging dedup |
274
+ | **Array Methods** | Simple transformations | Result formatting |
275
+ | **Sequential** | Memory-constrained | Mobile search |
276
+ | **Parallel** | Speed needed, memory available | Desktop search |
277
+ | **Mutable State** | Performance critical | Batch accumulation |
278
+
279
+ ---
280
+
281
+ ## Key Takeaways
282
+
283
+ 1. **Functional for data** - Transformations, scoring, formatting
284
+ 2. **Imperative for control** - Complex loops, performance, memory management
285
+ 3. **Async for I/O** - Database, files, network
286
+ 4. **Pure when possible** - Easier to test and reason about
287
+ 5. **Mutable when necessary** - But isolate the mutation
288
+
289
+ The codebase prioritizes **pragmatism over purity** - using whatever pattern solves the problem best while keeping the code readable and maintainable.