amalfa 1.0.19 → 1.0.22

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "amalfa",
3
- "version": "1.0.19",
3
+ "version": "1.0.22",
4
4
  "description": "Local-first knowledge graph engine for AI agents. Transforms markdown into searchable memory with MCP protocol.",
5
5
  "license": "MIT",
6
6
  "homepage": "https://github.com/pjsvis/amalfa#readme",
@@ -12,6 +12,13 @@
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  "type": "git",
13
13
  "url": "git+https://github.com/pjsvis/amalfa.git"
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  },
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+ "main": "src/cli.ts",
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+ "type": "module",
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+ "files": [
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+ "src",
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+ "README.md",
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+ "LICENSE"
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+ ],
15
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  "keywords": [
16
23
  "mcp",
17
24
  "model-context-protocol",
@@ -51,11 +58,11 @@
51
58
  "stats": "bun run src/cli.ts stats",
52
59
  "doctor": "bun run src/cli.ts doctor",
53
60
  "daemon": "bun run src/cli.ts daemon status",
54
- "help": "bun run src/cli.ts --help"
61
+ "help": "bun run src/cli.ts --help",
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+ "publish": "npm publish"
55
63
  },
56
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  "dependencies": {
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  "@modelcontextprotocol/sdk": "1.25.0",
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- "amalfa": "^1.0.18",
59
66
  "fastembed": "2.0.0",
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  "pino": "^10.1.0"
61
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  }
package/src/cli.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  #!/usr/bin/env bun
2
- import { existsSync, statSync } from "node:fs";
3
- import { join } from "node:path";
4
- import { spawn } from "node:child_process";
2
+ import { existsSync, statSync } from "fs";
3
+ import { join } from "path";
4
+ import { spawn } from "child_process";
5
5
  import pkg from "../package.json" with { type: "json" };
6
6
 
7
7
  const VERSION = pkg.version;
@@ -3,8 +3,8 @@
3
3
  * Default settings that can be overridden via amalfa.config.{ts,js,json}
4
4
  */
5
5
 
6
- import { mkdirSync, existsSync } from "node:fs";
7
- import { join } from "node:path";
6
+ import { mkdirSync, existsSync } from "fs";
7
+ import { join } from "path";
8
8
 
9
9
  /** AMALFA directory structure */
10
10
  export const AMALFA_DIRS = {
@@ -1,4 +1,4 @@
1
- import { randomUUID } from "node:crypto";
1
+ import { randomUUID } from "crypto";
2
2
 
3
3
  export class MarkdownMasker {
4
4
  private stash: Map<string, string> = new Map();
@@ -4,9 +4,9 @@
4
4
  * File watcher for incremental database updates
5
5
  */
6
6
 
7
- import { existsSync } from "node:fs";
8
- import { watch } from "node:fs";
9
- import { join } from "node:path";
7
+ import { existsSync } from "fs";
8
+ import { watch } from "fs";
9
+ import { join } from "path";
10
10
  import { loadConfig, AMALFA_DIRS } from "@src/config/defaults";
11
11
  import { AmalfaIngestor } from "@src/pipeline/AmalfaIngestor";
12
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  import { ResonanceDB } from "@src/resonance/db";
package/src/mcp/index.ts CHANGED
@@ -1,5 +1,5 @@
1
- import { appendFileSync } from "node:fs";
2
- import { join } from "node:path";
1
+ import { appendFileSync } from "fs";
2
+ import { join } from "path";
3
3
  import { Server } from "@modelcontextprotocol/sdk/server/index.js";
4
4
  import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
5
5
  import {
@@ -8,13 +8,12 @@ import {
8
8
  ListToolsRequestSchema,
9
9
  ReadResourceRequestSchema,
10
10
  } from "@modelcontextprotocol/sdk/types.js";
11
- import { loadConfig } from "@src/config/defaults";
11
+ import { AMALFA_DIRS, loadConfig } from "@src/config/defaults";
12
12
  import { VectorEngine } from "@src/core/VectorEngine";
13
13
  import { ResonanceDB } from "@src/resonance/db";
14
14
  import { DaemonManager } from "../utils/DaemonManager";
15
15
  import { getLogger } from "../utils/Logger";
16
16
  import { ServiceLifecycle } from "../utils/ServiceLifecycle";
17
- import { AMALFA_DIRS } from "@src/config/defaults";
18
17
 
19
18
  const args = process.argv.slice(2);
20
19
  const command = args[0] || "serve";
@@ -296,10 +295,7 @@ async function runServer() {
296
295
 
297
296
  if (name === TOOLS.LIST) {
298
297
  // TODO: Make this configurable via amalfa.config.ts
299
- const structure = [
300
- "docs/",
301
- "notes/",
302
- ];
298
+ const structure = ["docs/", "notes/"];
303
299
  return {
304
300
  content: [{ type: "text", text: JSON.stringify(structure, null, 2) }],
305
301
  };
@@ -308,17 +304,37 @@ async function runServer() {
308
304
  if (name === TOOLS.GARDEN) {
309
305
  const filePath = String(args?.file_path);
310
306
  const tags = args?.tags as string[];
311
- const content = await Bun.file(filePath).text();
312
- const tagBlock = `\n<!-- tags: ${tags.join(", ")} -->\n`;
313
- const newContent = content.endsWith("\n")
314
- ? content + tagBlock
315
- : `${content}\n${tagBlock}`;
316
- await Bun.write(filePath, newContent);
307
+ let content = await Bun.file(filePath).text();
308
+
309
+ // Check for existing tag block and merge/replace
310
+ const tagPattern = /<!-- tags: ([^>]+) -->\s*$/;
311
+ const match = content.match(tagPattern);
312
+
313
+ let operation = "injected";
314
+ if (match?.[1]) {
315
+ // Merge with existing tags
316
+ const existingTags = match[1]
317
+ .split(",")
318
+ .map((t) => t.trim())
319
+ .filter(Boolean);
320
+ const mergedTags = [...new Set([...existingTags, ...tags])]; // deduplicate
321
+ const tagBlock = `<!-- tags: ${mergedTags.join(", ")} -->`;
322
+ content = content.replace(tagPattern, `${tagBlock}\n`);
323
+ operation = "merged";
324
+ } else {
325
+ // Append new tag block
326
+ const tagBlock = `<!-- tags: ${tags.join(", ")} -->`;
327
+ content = content.endsWith("\n")
328
+ ? `${content}\n${tagBlock}\n`
329
+ : `${content}\n\n${tagBlock}\n`;
330
+ }
331
+
332
+ await Bun.write(filePath, content);
317
333
  return {
318
334
  content: [
319
335
  {
320
336
  type: "text",
321
- text: `Injected ${tags.length} tags into ${filePath}`,
337
+ text: `Successfully ${operation} ${tags.length} tags into ${filePath}`,
322
338
  },
323
339
  ],
324
340
  };
@@ -4,14 +4,14 @@
4
4
  * No Persona/CDA complexity - just pure markdown → knowledge graph
5
5
  */
6
6
 
7
- import { join } from "node:path";
8
- import { Glob } from "bun";
7
+ import { join } from "path";
9
8
  import type { AmalfaConfig } from "@src/config/defaults";
10
9
  import { EdgeWeaver } from "@src/core/EdgeWeaver";
11
- import { ResonanceDB, type Node } from "@src/resonance/db";
10
+ import type { Node, ResonanceDB } from "@src/resonance/db";
12
11
  import { Embedder } from "@src/resonance/services/embedder";
13
12
  import { SimpleTokenizerService as TokenizerService } from "@src/resonance/services/simpleTokenizer";
14
13
  import { getLogger } from "@src/utils/Logger";
14
+ import { Glob } from "bun";
15
15
 
16
16
  export interface IngestionResult {
17
17
  success: boolean;
@@ -37,7 +37,7 @@ export class AmalfaIngestor {
37
37
  */
38
38
  async ingest(): Promise<IngestionResult> {
39
39
  const startTime = performance.now();
40
-
40
+
41
41
  const sources = this.config.sources || ["./docs"];
42
42
  this.log.info(`📚 Starting ingestion from: ${sources.join(", ")}`);
43
43
 
@@ -47,7 +47,7 @@ export class AmalfaIngestor {
47
47
  await embedder.embed("init"); // Warm up
48
48
 
49
49
  const tokenizer = TokenizerService.getInstance();
50
-
50
+
51
51
  // Discover markdown files
52
52
  const files = await this.discoverFiles();
53
53
  this.log.info(`📁 Found ${files.length} markdown files`);
@@ -108,7 +108,10 @@ export class AmalfaIngestor {
108
108
  if (!filePath) continue;
109
109
  const content = await Bun.file(filePath).text();
110
110
  const filename = filePath.split("/").pop() || "unknown";
111
- const id = filename.replace(".md", "").toLowerCase().replace(/[^a-z0-9-]/g, "-");
111
+ const id = filename
112
+ .replace(".md", "")
113
+ .toLowerCase()
114
+ .replace(/[^a-z0-9-]/g, "-");
112
115
  weaver.weave(id, content);
113
116
  }
114
117
  this.db.commit();
@@ -117,17 +120,36 @@ export class AmalfaIngestor {
117
120
  this.log.info("💾 Forcing WAL checkpoint...");
118
121
  this.db.getRawDb().run("PRAGMA wal_checkpoint(TRUNCATE);");
119
122
 
123
+ // OH-104: The Pinch Check (verify physical commit)
124
+ const dbPath = this.db.getRawDb().filename;
125
+ const dbFile = Bun.file(dbPath);
126
+ if (!(await dbFile.exists())) {
127
+ throw new Error(
128
+ "OH-104 VIOLATION: Database file missing after checkpoint",
129
+ );
130
+ }
131
+ const finalSize = dbFile.size;
132
+ if (finalSize === 0) {
133
+ throw new Error(
134
+ "OH-104 VIOLATION: Database file is empty after checkpoint",
135
+ );
136
+ }
137
+ this.log.info(`✅ Pinch Check: db=${(finalSize / 1024).toFixed(1)}KB`);
138
+
120
139
  const endTime = performance.now();
121
140
  const durationSec = (endTime - startTime) / 1000;
122
141
 
123
142
  const stats = this.db.getStats();
124
- this.log.info({
125
- files: processedCount,
126
- nodes: stats.nodes,
127
- edges: stats.edges,
128
- vectors: stats.vectors,
129
- durationSec: durationSec.toFixed(2),
130
- }, "✅ Ingestion complete");
143
+ this.log.info(
144
+ {
145
+ files: processedCount,
146
+ nodes: stats.nodes,
147
+ edges: stats.edges,
148
+ vectors: stats.vectors,
149
+ durationSec: durationSec.toFixed(2),
150
+ },
151
+ "✅ Ingestion complete",
152
+ );
131
153
 
132
154
  return {
133
155
  success: true,
@@ -178,7 +200,10 @@ export class AmalfaIngestor {
178
200
  }
179
201
  }
180
202
  } catch (e) {
181
- this.log.warn({ source: sourcePath, err: e }, "⚠️ Failed to scan directory");
203
+ this.log.warn(
204
+ { source: sourcePath, err: e },
205
+ "⚠️ Failed to scan directory",
206
+ );
182
207
  }
183
208
  }
184
209
 
@@ -215,9 +240,7 @@ export class AmalfaIngestor {
215
240
 
216
241
  // Parse frontmatter
217
242
  const fmMatch = content.match(/^---\n([\s\S]*?)\n---/);
218
- const frontmatter = fmMatch?.[1]
219
- ? this.parseFrontmatter(fmMatch[1])
220
- : {};
243
+ const frontmatter = fmMatch?.[1] ? this.parseFrontmatter(fmMatch[1]) : {};
221
244
 
222
245
  // Generate ID from filename
223
246
  const filename = filePath.split("/").pop() || "unknown";
@@ -10,8 +10,8 @@
10
10
  * Generates .amalfa/logs/pre-flight.log with recommendations.
11
11
  */
12
12
 
13
- import { existsSync, lstatSync, readdirSync, realpathSync, statSync, writeFileSync } from "node:fs";
14
- import { join, relative } from "node:path";
13
+ import { existsSync, lstatSync, readdirSync, realpathSync, statSync, writeFileSync } from "fs";
14
+ import { join, relative } from "path";
15
15
  import { getLogger } from "@src/utils/Logger";
16
16
  import type { AmalfaConfig } from "@src/config/defaults";
17
17
  import { AMALFA_DIRS, initAmalfaDirs } from "@src/config/defaults";
@@ -10,8 +10,8 @@
10
10
  * await harvester.loadIntoResonance(graph);
11
11
  */
12
12
 
13
- import { existsSync } from "node:fs";
14
- import { join } from "node:path";
13
+ import { existsSync } from "fs";
14
+ import { join } from "path";
15
15
  import { getLogger } from "@src/utils/Logger";
16
16
  import { $ } from "bun";
17
17
 
@@ -1,4 +1,4 @@
1
- import { join } from "node:path";
1
+ import { join } from "path";
2
2
  import { toFafcas } from "@src/resonance/db";
3
3
  import { EmbeddingModel, FlagEmbedding } from "fastembed";
4
4
 
@@ -5,7 +5,7 @@
5
5
  */
6
6
 
7
7
  import { serve } from "bun";
8
- import { join } from "node:path";
8
+ import { join } from "path";
9
9
  import { EmbeddingModel, FlagEmbedding } from "fastembed";
10
10
  import { toFafcas } from "@src/resonance/db";
11
11
  import { getLogger } from "@src/utils/Logger";
@@ -1,5 +1,5 @@
1
- import { existsSync } from "node:fs";
2
- import { join } from "node:path";
1
+ import { existsSync } from "fs";
2
+ import { join } from "path";
3
3
  import { ServiceLifecycle } from "./ServiceLifecycle";
4
4
  import { AMALFA_DIRS } from "@src/config/defaults";
5
5
 
@@ -1,5 +1,5 @@
1
- import { spawn } from "node:child_process";
2
- import { platform } from "node:os";
1
+ import { spawn } from "child_process";
2
+ import { platform } from "os";
3
3
 
4
4
  /**
5
5
  * Send a native desktop notification
@@ -1,6 +1,6 @@
1
- import { existsSync } from "node:fs";
2
- import { unlink } from "node:fs/promises";
3
- import { join } from "node:path";
1
+ import { existsSync } from "fs";
2
+ import { unlink } from "fs/promises";
3
+ import { join } from "path";
4
4
  import { ZombieDefense } from "./ZombieDefense";
5
5
  import { AMALFA_DIRS, initAmalfaDirs } from "@src/config/defaults";
6
6
 
@@ -1,5 +1,5 @@
1
- import { existsSync, mkdirSync } from "node:fs";
2
- import { join } from "node:path";
1
+ import { existsSync, mkdirSync } from "fs";
2
+ import { join } from "path";
3
3
  import { AMALFA_DIRS } from "@src/config/defaults";
4
4
 
5
5
  export interface DatabaseSnapshot {
@@ -1,5 +1,5 @@
1
- import { exec } from "node:child_process";
2
- import { promisify } from "node:util";
1
+ import { exec } from "child_process";
2
+ import { promisify } from "util";
3
3
 
4
4
  const execAsync = promisify(exec);
5
5
 
package/.biomeignore DELETED
@@ -1,19 +0,0 @@
1
- **/*-bak.html
2
- **/*.bak
3
- public/layout-test.html
4
- public/test
5
- public/js
6
- public/css/app.css
7
- node_modules
8
- dist
9
- .DS_Store
10
- **/*.py
11
- **/*.c
12
- **/*.cpp
13
- **/*.h
14
- **/*.hpp
15
- **/*.sh
16
- **/*.txt
17
- docs
18
- examples
19
- experiments
@@ -1,113 +0,0 @@
1
- /**
2
- * AMALFA Configuration Example
3
- *
4
- * Copy this file to your project root as:
5
- * - amalfa.config.ts (TypeScript)
6
- * - amalfa.config.js (JavaScript)
7
- * - amalfa.config.json (JSON)
8
- */
9
-
10
- export default {
11
- /**
12
- * Source directories containing markdown files
13
- * Relative to project root
14
- *
15
- * Examples:
16
- * - ["./docs"] - Single directory
17
- * - ["./docs", "./notes"] - Multiple directories
18
- * - ["./docs", "../shared/notes"] - Across repositories
19
- * - ["."] - Current directory (scans all .md files)
20
- *
21
- * Legacy: Single 'source' string still supported for backward compatibility
22
- */
23
- sources: ["./docs"],
24
-
25
- /**
26
- * Database file location
27
- * Relative to project root
28
- *
29
- * The .amalfa directory is gitignored by default.
30
- * The database can be regenerated from markdown at any time.
31
- */
32
- database: ".amalfa/resonance.db",
33
-
34
- /**
35
- * Embedding configuration
36
- */
37
- embeddings: {
38
- /**
39
- * Embedding model to use
40
- *
41
- * Options:
42
- * - "BAAI/bge-small-en-v1.5" (default) - Best balance (384 dims)
43
- * - "sentence-transformers/all-MiniLM-L6-v2" - Faster (384 dims)
44
- * - "BAAI/bge-base-en-v1.5" - More accurate (768 dims, slower)
45
- *
46
- * Models are downloaded on first use to .resonance/cache/
47
- */
48
- model: "BAAI/bge-small-en-v1.5",
49
-
50
- /**
51
- * Vector dimensions
52
- * Must match the model's output size
53
- *
54
- * Common dimensions:
55
- * - 384: Most small models
56
- * - 768: Most base models
57
- * - 1024: Large models
58
- */
59
- dimensions: 384,
60
- },
61
-
62
- /**
63
- * File watcher configuration
64
- */
65
- watch: {
66
- /**
67
- * Enable file watching
68
- * Used by 'amalfa daemon' command
69
- */
70
- enabled: true,
71
-
72
- /**
73
- * Debounce delay in milliseconds
74
- *
75
- * How long to wait after the last file change before
76
- * triggering re-ingestion. This prevents excessive
77
- * processing during rapid file edits.
78
- *
79
- * Recommended:
80
- * - 1000ms (1 second) - Default, good for most cases
81
- * - 500ms - More responsive, slightly higher CPU
82
- * - 2000ms - Less responsive, lower CPU
83
- */
84
- debounce: 1000,
85
-
86
- /**
87
- * Show desktop notifications
88
- *
89
- * When enabled, the daemon sends native OS notifications
90
- * when the knowledge graph is updated.
91
- *
92
- * Default: true
93
- * Set to false for silent operation
94
- */
95
- notifications: true,
96
- },
97
-
98
- /**
99
- * Patterns to exclude from ingestion
100
- *
101
- * Files/directories matching these patterns are ignored.
102
- * Patterns are checked with String.includes(), not glob.
103
- *
104
- * Common exclusions:
105
- * - "node_modules" - JavaScript dependencies
106
- * - ".git" - Git internals
107
- * - ".amalfa" - AMALFA data directory
108
- * - "vendor" - PHP dependencies
109
- * - "target" - Rust build artifacts
110
- * - "dist" - Build output
111
- */
112
- excludePatterns: ["node_modules", ".git", ".amalfa"],
113
- };
package/biome.json DELETED
@@ -1,49 +0,0 @@
1
- {
2
- "$schema": "https://biomejs.dev/schemas/2.3.8/schema.json",
3
- "vcs": {
4
- "enabled": true,
5
- "clientKind": "git",
6
- "useIgnoreFile": true
7
- },
8
- "files": {
9
- "ignoreUnknown": false,
10
- "includes": [
11
- "src/**",
12
- "scripts/**",
13
- "tests/**",
14
- "*.ts",
15
- "*.js",
16
- "*.json",
17
- "*.css"
18
- ]
19
- },
20
- "formatter": {
21
- "enabled": true,
22
- "indentStyle": "tab"
23
- },
24
- "linter": {
25
- "enabled": true,
26
- "rules": {
27
- "recommended": true
28
- }
29
- },
30
- "javascript": {
31
- "formatter": {
32
- "quoteStyle": "double"
33
- }
34
- },
35
- "css": {
36
- "parser": {
37
- "cssModules": true,
38
- "tailwindDirectives": true
39
- }
40
- },
41
- "assist": {
42
- "enabled": true,
43
- "actions": {
44
- "source": {
45
- "organizeImports": "on"
46
- }
47
- }
48
- }
49
- }
package/bun.lock DELETED
@@ -1,369 +0,0 @@
1
- {
2
- "lockfileVersion": 1,
3
- "workspaces": {
4
- "": {
5
- "name": "polyvis",
6
- "dependencies": {
7
- "@modelcontextprotocol/sdk": "1.25.0",
8
- "amalfa": "^1.0.17",
9
- "fastembed": "2.0.0",
10
- "pino": "^10.1.0",
11
- },
12
- "devDependencies": {
13
- "@biomejs/biome": "2.3.8",
14
- "@types/bun": "1.3.4",
15
- "only-allow": "^1.2.2",
16
- "pino-pretty": "^13.1.3",
17
- },
18
- },
19
- },
20
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package/tsconfig.json DELETED
@@ -1,46 +0,0 @@
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- {
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- "compilerOptions": {
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- // Environment setup & latest features
4
- "lib": ["ESNext"],
5
- "target": "ESNext",
6
- "module": "Preserve",
7
- "moduleDetection": "force",
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- "jsx": "react-jsx",
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- // Bundler mode
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- "allowImportingTsExtensions": true,
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- "verbatimModuleSyntax": true,
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- "noEmit": true,
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-
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- // Best practices
18
- "strict": true,
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- "skipLibCheck": true,
20
- "noFallthroughCasesInSwitch": true,
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- "noUncheckedIndexedAccess": true,
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- "noImplicitOverride": true,
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-
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- // Some stricter flags (disabled by default)
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- "noPropertyAccessFromIndexSignature": false,
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- "baseUrl": ".",
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- ".resonance",
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- "briefs",
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- "examples",
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- "experiments"
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- ]
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