@mnemonik/shared 5.33.12 → 5.75.3

package/dist/codeScanner.d.ts

@@ -23,6 +23,12 @@ export interface ScanOptions {
     ignorePatterns?: string[];
     includeExtensions?: string[];
 }
+/**
+ * Matchers for authority manifest / config / CI files whose verbatim content
+ * is collected by `collectAuthorityFiles` and pushed to the server for
+ * doc-truth Fingerprint parsing. Operates on relative, forward-slash paths.
+ */
+export declare const AUTHORITY_FILE_MATCHERS: Array<(relPath: string) => boolean>;
 export declare class CodeScanner {
     private options;
     constructor(options?: ScanOptions);
@@ -36,6 +42,24 @@ export declare class CodeScanner {
      * Added max depth (10) to prevent infinite recursion
      */
     scanDirectory(rootPath: string): Promise<CodeChunk[]>;
+    /**
+     * Enumerate scan-eligible relative file paths under `rootPath` without
+     * reading or chunking content. Same walk + ignorePatterns + extension
+     * filter as `scanDirectory`, but bounded to O(file count) directory ops
+     * — cheap enough to call on every periodic reconcile tick.
+     *
+     * Returns relative paths normalized against `rootPath`, matching the
+     * shape the server stores in `memories.metadata->>'filePath'`. Use this
+     * for the scanner reconciliation channel (`POST /api/v1/scan/reconcile`).
+     *
+     * Defensive: skips any path whose `relative()` result contains a `..`
+     * traversal segment (can happen when a symlink resolves under root but
+     * the readdir entry path doesn't normalize cleanly). The server's
+     * `safeScanPath` rejects such paths; filtering here keeps a single
+     * malformed entry from failing the entire reconcile push.
+     */
+    listFiles(rootPath: string): Promise<string[]>;
+    private traversePaths;
     /**
      * Scan specific files and extract code chunks.
      * Pass rootPath to compute proper relative file paths in chunk metadata.
@@ -104,5 +128,15 @@ export declare class CodeScanner {
      * Generate content hash for drift detection
      */
     private hash;
+    /**
+     * Walk the project for authority manifest/config/CI files and return their
+     * verbatim content. Reuses ignorePatterns; matches AUTHORITY_FILE_MATCHERS
+     * (not includeExtensions). Content-only — no chunking, no embeddings.
+     */
+    collectAuthorityFiles(projectRoot: string): Promise<Array<{
+        path: string;
+        content: string;
+        hash: string;
+    }>>;
 }
 //# sourceMappingURL=codeScanner.d.ts.map

package/dist/codeScanner.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"codeScanner.d.ts","sourceRoot":"","sources":["../src/codeScanner.ts"],"names":[],"mappings":"AAAA;;GAEG;AAcH,MAAM,WAAW,SAAS;IACxB,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,UAAU,GAAG,OAAO,GAAG,QAAQ,GAAG,KAAK,CAAC;IACnD,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE;QACR,QAAQ,EAAE,MAAM,CAAC;QACjB,SAAS,EAAE,MAAM,CAAC;QAClB,IAAI,EAAE,MAAM,CAAC;QACb,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,UAAU,CAAC,EAAE,MAAM,CAAC;KACrB,CAAC;CACH;AAED,MAAM,WAAW,WAAW;IAC1B,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B,iBAAiB,CAAC,EAAE,MAAM,EAAE,CAAC;CAC9B;AAsED;;;;GAIG;AACH,eAAO,MAAM,uBAAuB,EAAE,KAAK,CAAC,CAAC,OAAO,EAAE,MAAM,KAAK,OAAO,CAiBvE,CAAC;AAEF,qBAAa,WAAW;IACtB,OAAO,CAAC,OAAO,CAAwB;gBAE3B,OAAO,GAAE,WAAgB;IAIrC;;;OAGG;IACH,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAM;IAEvC;;;OAGG;IACG,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC;IAM3D;;;;;;;;;;;;;;;OAeG;IACG,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;YAMtC,aAAa;IA6C3B;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC;IAoC5E;;;OAGG;YACW,iBAAiB;IA+D/B;;;;;;;OAOG;IACH,OAAO,CAAC,YAAY;IAepB;;;OAGG;IACH,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAoB;YAE3C,SAAS;IAyFvB;;OAEG;IACH,OAAO,CAAC,cAAc;IAwBtB;;OAEG;IACH,OAAO,CAAC,aAAa;IAoFrB;;;;OAIG;IACH,OAAO,CAAC,iBAAiB;IA0GzB;;;OAGG;IACH,OAAO,CAAC,uBAAuB;IAoE/B;;OAEG;IACH,OAAO,CAAC,mBAAmB;IAqD3B;;;;;;;;;;;;;;OAcG;IACH,OAAO,CAAC,QAAQ;IA2FhB;;OAEG;IACH,OAAO,CAAC,IAAI;IAIZ;;;;OAIG;IACG,qBAAqB,CACzB,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CAoCnE"}

package/dist/codeScanner.js

@@ -2,7 +2,7 @@
  * Code Scanner - Parse and chunk source files for embedding
  */
 import { readdir, readFile, stat, lstat, realpath } from 'fs/promises';
-import { join, relative, extname } from 'path';
+import { join, relative, extname, sep } from 'path';
 import { createHash } from 'crypto';
 import { debug as logDebug } from './logger.js';
 import { withTimeout } from './asyncUtils.js';
@@ -49,6 +49,14 @@ const DEFAULT_OPTIONS = {
         '*.bundle.js',
         '*.legacy.js',
         '*.map',
+        // Agent-host transient checkouts. EnterWorktree creates isolated git
+        // worktree copies under `.claude/worktrees/{name}/`; indexing them
+        // duplicates the entire codebase under a path that misclassifies as
+        // `archive` doctype and polluted the dogfood corpus with 376 stale
+        // couplings. Glob form (with `*`) so the regex matcher applies it as a
+        // path predicate rather than a path-segment-equality predicate (which
+        // would not match the nested form).
+        '.claude/worktrees/*',
     ],
     includeExtensions: [
         '.ts',
@@ -70,6 +78,29 @@ const DEFAULT_OPTIONS = {
         '.md',
     ],
 };
+/**
+ * Matchers for authority manifest / config / CI files whose verbatim content
+ * is collected by `collectAuthorityFiles` and pushed to the server for
+ * doc-truth Fingerprint parsing. Operates on relative, forward-slash paths.
+ */
+export const AUTHORITY_FILE_MATCHERS = [
+    (p) => p === 'package.json',
+    (p) => /^(packages|apps|services|tools)\/[^/]+\/package\.json$/.test(p),
+    (p) => p === 'tsconfig.json' || /^tsconfig\.[^/]+\.json$/.test(p),
+    (p) => p === 'pyproject.toml',
+    (p) => p === 'requirements.txt',
+    (p) => p === 'setup.py',
+    (p) => p === 'Cargo.toml',
+    (p) => p === 'Gemfile',
+    (p) => p === 'Makefile',
+    (p) => p === '.env.example',
+    (p) => /^\.github\/workflows\/[^/]+\.(yml|yaml)$/.test(p),
+    // SQL migrations: the schema_columns authority extractor reads every .sql
+    // under `migrations/` (listFiles('migrations/') -> LIKE 'migrations/%' then
+    // .endsWith('.sql')). Without collecting these, that authority is empty and
+    // every schema_table_enumeration claim falls to unverifiable.
+    (p) => /^migrations\/.*\.sql$/.test(p),
+];
 export class CodeScanner {
     options;
     constructor(options = {}) {
@@ -89,6 +120,61 @@ export class CodeScanner {
         await this.traverseDirectory(rootPath, rootPath, chunks, 0);
         return chunks;
     }
+    /**
+     * Enumerate scan-eligible relative file paths under `rootPath` without
+     * reading or chunking content. Same walk + ignorePatterns + extension
+     * filter as `scanDirectory`, but bounded to O(file count) directory ops
+     * — cheap enough to call on every periodic reconcile tick.
+     *
+     * Returns relative paths normalized against `rootPath`, matching the
+     * shape the server stores in `memories.metadata->>'filePath'`. Use this
+     * for the scanner reconciliation channel (`POST /api/v1/scan/reconcile`).
+     *
+     * Defensive: skips any path whose `relative()` result contains a `..`
+     * traversal segment (can happen when a symlink resolves under root but
+     * the readdir entry path doesn't normalize cleanly). The server's
+     * `safeScanPath` rejects such paths; filtering here keeps a single
+     * malformed entry from failing the entire reconcile push.
+     */
+    async listFiles(rootPath) {
+        const paths = [];
+        await this.traversePaths(rootPath, rootPath, paths, 0);
+        return paths.filter((p) => !/(^|[/\\])\.\.([/\\]|$)/.test(p));
+    }
+    async traversePaths(currentPath, rootPath, out, depth) {
+        if (depth >= CodeScanner.MAX_DEPTH)
+            return;
+        try {
+            const entries = await withTimeout(readdir(currentPath), FILE_OP_TIMEOUT_MS, `readdir timed out: ${currentPath}`);
+            for (const entry of entries) {
+                const fullPath = join(currentPath, entry);
+                const relativePath = relative(rootPath, fullPath);
+                if (this.shouldIgnore(relativePath))
+                    continue;
+                const lstats = await withTimeout(lstat(fullPath), FILE_OP_TIMEOUT_MS, `lstat timed out: ${fullPath}`);
+                if (lstats.isSymbolicLink()) {
+                    const resolved = await realpath(fullPath);
+                    const resolvedRoot = await realpath(rootPath);
+                    if (!resolved.startsWith(resolvedRoot + '/') && resolved !== resolvedRoot)
+                        continue;
+                }
+                const stats = lstats.isSymbolicLink()
+                    ? await withTimeout(stat(fullPath), FILE_OP_TIMEOUT_MS, `stat timed out: ${fullPath}`)
+                    : lstats;
+                if (stats.isDirectory()) {
+                    await this.traversePaths(fullPath, rootPath, out, depth + 1);
+                }
+                else if (stats.isFile()) {
+                    if (this.options.includeExtensions.includes(extname(fullPath))) {
+                        out.push(relativePath);
+                    }
+                }
+            }
+        }
+        catch (error) {
+            logDebug('Error traversing directory (listFiles)', { path: currentPath, error });
+        }
+    }
     /**
      * Scan specific files and extract code chunks.
      * Pass rootPath to compute proper relative file paths in chunk metadata.
@@ -700,5 +786,50 @@ export class CodeScanner {
     hash(content) {
         return createHash('sha256').update(content).digest('hex').substring(0, 16);
     }
+    /**
+     * Walk the project for authority manifest/config/CI files and return their
+     * verbatim content. Reuses ignorePatterns; matches AUTHORITY_FILE_MATCHERS
+     * (not includeExtensions). Content-only — no chunking, no embeddings.
+     */
+    async collectAuthorityFiles(projectRoot) {
+        const out = [];
+        // M2: cap walk depth to match the scanner's MAX_DEPTH (10)
+        const walk = async (dir, depth) => {
+            if (depth >= CodeScanner.MAX_DEPTH)
+                return;
+            let entries;
+            try {
+                entries = await readdir(dir, { withFileTypes: true });
+            }
+            catch {
+                return;
+            }
+            for (const ent of entries) {
+                const full = join(dir, ent.name);
+                const rel = relative(projectRoot, full).split(sep).join('/');
+                if (this.shouldIgnore(rel))
+                    continue;
+                if (ent.isDirectory()) {
+                    await walk(full, depth + 1);
+                }
+                else if (AUTHORITY_FILE_MATCHERS.some((m) => m(rel))) {
+                    try {
+                        const content = await readFile(full, 'utf-8');
+                        // C2: skip files whose content exceeds the server's 5MB cap —
+                        // manifests are tiny; an oversized one is anomalous.
+                        if (content.length > 5_000_000)
+                            continue;
+                        const hash = createHash('sha256').update(content).digest('hex');
+                        out.push({ path: rel, content, hash });
+                    }
+                    catch {
+                        /* unreadable — skip */
+                    }
+                }
+            }
+        };
+        await walk(projectRoot, 0);
+        return out;
+    }
 }
 //# sourceMappingURL=codeScanner.js.map

package/dist/codeScanner.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -6,7 +6,7 @@
  */
 export { MCP_INSTRUCTIONS, MCP_INSTRUCTIONS_RAW, getMcpInstructions } from './instructions.js';
 export { USAGE_GUIDE } from './usageGuide.js';
-export { CodeScanner, type CodeChunk, type ScanOptions } from './codeScanner.js';
+export { CodeScanner, AUTHORITY_FILE_MATCHERS, type CodeChunk, type ScanOptions, } from './codeScanner.js';
 export { FileSystemReader, getFileSystemReader, type ScanFilesResult, type ChangedFilesResult, type FileData, } from './FileSystemReader.js';
 export { SECRET_PATTERNS, SECRET_REDACTION_PLACEHOLDER, scrubSecrets } from './secretPatterns.js';
 export { FETCH_TIMEOUT_MS, TELEMETRY_TIMEOUT_MS, POST_TOOL_TIMEOUT_MS, MCP_PRECHECK_TIMEOUT_MS, withHookTimeout, } from './hookTimeouts.js';

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EAAE,WAAW,EAAE,KAAK,SAAS,EAAE,KAAK,WAAW,EAAE,MAAM,kBAAkB,CAAC;AACjF,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,QAAQ,GACd,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EACL,WAAW,EACX,uBAAuB,EACvB,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,QAAQ,GACd,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}

package/dist/index.js

@@ -6,7 +6,7 @@
  */
 export { MCP_INSTRUCTIONS, MCP_INSTRUCTIONS_RAW, getMcpInstructions } from './instructions.js';
 export { USAGE_GUIDE } from './usageGuide.js';
-export { CodeScanner } from './codeScanner.js';
+export { CodeScanner, AUTHORITY_FILE_MATCHERS, } from './codeScanner.js';
 export { FileSystemReader, getFileSystemReader, } from './FileSystemReader.js';
 export { SECRET_PATTERNS, SECRET_REDACTION_PLACEHOLDER, scrubSecrets } from './secretPatterns.js';
 export { FETCH_TIMEOUT_MS, TELEMETRY_TIMEOUT_MS, POST_TOOL_TIMEOUT_MS, MCP_PRECHECK_TIMEOUT_MS, withHookTimeout, } from './hookTimeouts.js';

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EAAE,WAAW,EAAoC,MAAM,kBAAkB,CAAC;AACjF,OAAO,EACL,gBAAgB,EAChB,mBAAmB,GAIpB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EACL,WAAW,EACX,uBAAuB,GAGxB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,GAIpB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}

package/dist/instructions.d.ts

@@ -4,8 +4,22 @@
  * This is the SINGLE SOURCE OF TRUTH for MCP instructions.
  * Shared instruction content imported by the server.
  *
- * Version: 2.93
- * Updated: 2026-05-15
+ * Version: 2.98
+ * Updated: 2026-05-27
+ *
+ * v2.98 — Doc truth contracts are the normal drift surface. linkedDocs and
+ *         doc_code_couplings remain legacy diagnostics only; docs drift
+ *         defaults to truth findings and legacy:true is explicit debug.
+ * v2.97 — Dropped legacy doc-coupling action guidance. Coupling rows are
+ *         not truth findings (plan §1).
+ * v2.96 — Replace conditional memory_discover guidance with structural fix:
+ *         bootstrap now includes _methodCatalog (discoverMemoryTools({})) so
+ *         agents have the memory_tools calling convention from turn one.
+ *         Instruction updated to reference _methodCatalog directly.
+ * v2.95 — Drop `augments` from JIT directive verdict list per plan §5 default
+ *         (augments downgrades to ambient via the parallel recall gate, not
+ *         the directive lane). See jit-knowledge-injector.md §5 decision note.
+ * v2.94 — Add JIT directive teaching (docs/development/jit-knowledge-injector.md §2.3).
  *
  * Code mode permanent — all memory operations via memory_tools sandbox.
  *        memory_add, file_context etc. are now mnemonik.* methods, not standalone tools.
@@ -30,7 +44,7 @@ export declare function getMcpInstructions(): string;
  * Raw instructions content (always returns the content, ignores env var).
  * Use getMcpInstructions() for production code.
  */
-export declare const MCP_INSTRUCTIONS_RAW = "You have Mnemonik, a persistent memory system for this project.\n\nFirst call, every session: session_bootstrap. Read the mnemonik skill (from available_skills) for the full workflow.\nAfter bootstrap: execute _directive.message actions immediately (scanner daemon check is mandatory).\n\nUse memory_discover before memory_tools when you are unsure which mnemonik.* method to call, when a method has actions, or after a validation error.\nProactively call memory_search before starting new work \u2014 avoids rediscovering known patterns and contradicting past decisions.\nProactively call file_context before editing any file \u2014 loads past bugs, decisions, and gotchas for that file.\nProactively call checkpoint after making changes or decisions worth keeping \u2014 your context is ephemeral and checkpoint is the only way decisions survive across sessions and context compaction. Do not wait for the user to say \"done\" or \"thanks\".\n\nWhen mnemonik.file_context({ filePaths, cwd }) returns linkedDocs with driftStatus 'stale', update docs then call mnemonik.docs({ action: 'resolve', docPath, cwd }).\n\nAmbient envelopes contain background memories surfaced because they may be relevant to your current turn. Treat them as information, not directive. Weight them lower than your own reasoning unless they directly answer the question. They are advisory recall, not authoritative evidence.\n\nSkip: formatting-only, trivial one-line, mechanical refactors, git ops, tests.\nSave: architectural decisions, bug root causes, user preferences, discovered patterns, multi-file changes.";
+export declare const MCP_INSTRUCTIONS_RAW = "You have Mnemonik, a persistent memory system for this project.\n\nFirst call, every session: session_bootstrap. Read the mnemonik skill (from available_skills) for the full workflow.\nAfter bootstrap: execute _directive.message actions immediately (scanner daemon check is mandatory).\n\nThe bootstrap response includes _methodCatalog \u2014 the full list of mnemonik methods and the memory_tools calling convention. Read it before making any memory_tools calls. Use memory_discover({ method }) for the full schema and a copy-pasteable example of a specific method or action.\nProactively call memory_search before starting new work \u2014 avoids rediscovering known patterns and contradicting past decisions.\nProactively call file_context before editing any file \u2014 loads past bugs, decisions, and gotchas for that file.\nProactively call checkpoint after making changes or decisions worth keeping \u2014 your context is ephemeral and checkpoint is the only way decisions survive across sessions and context compaction. Do not wait for the user to say \"done\" or \"thanks\".\n\nDocumentation drift uses explicit doc-truth contracts. Treat _docDrift/docTruthFindings as actionable only when each finding includes a concrete assertion, named authority, observed mismatch, and agentAction='update_doc'. _docHealth, linkedDocs, stale-coupling counts, and docs({ action: 'drift', legacy: true }) are diagnostics only, not instructions to edit or resolve docs.\n\nAmbient envelopes contain background memories surfaced because they may be relevant to your current turn. Treat them as information, not directive. Weight them lower than your own reasoning unless they directly answer the question. They are advisory recall, not authoritative evidence.\n\nDirective envelopes with signal=\"jit_required\" are different from ambient. They surface memories that the server has classified as contradicting or materially refining the answer you were about to give to the current prompt. Each memory carries a verdict (contradicts | refines) and a one-line reason. Treat these as authoritative for the current response \u2014 comply with the surfaced fact unless it is clearly outdated or wrong. Do not silently route around them. If you disagree with a surfaced memory, say so explicitly and explain why; do not just ignore it.\n\nSkip: formatting-only, trivial one-line, mechanical refactors, git ops, tests.\nSave: architectural decisions, bug root causes, user preferences, discovered patterns, multi-file changes.";
 /**
  * Default export for convenience.
  * Note: This respects the MNEMONIK_INSTRUCTIONS_ENABLED env var.

package/dist/instructions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"instructions.d.ts","sourceRoot":"","sources":["../src/instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAmBH;;;;;;;;GAQG;AACH,wBAAgB,kBAAkB,IAAI,MAAM,CAO3C;AAED;;;GAGG;AACH,eAAO,MAAM,oBAAoB,4jDAAuB,CAAC;AAEzD;;;GAGG;AACH,eAAO,MAAM,gBAAgB,QAAuB,CAAC"}
+{"version":3,"file":"instructions.d.ts","sourceRoot":"","sources":["../src/instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAqBH;;;;;;;;GAQG;AACH,wBAAgB,kBAAkB,IAAI,MAAM,CAO3C;AAED;;;GAGG;AACH,eAAO,MAAM,oBAAoB,q9EAAuB,CAAC;AAEzD;;;GAGG;AACH,eAAO,MAAM,gBAAgB,QAAuB,CAAC"}

package/dist/instructions.js

@@ -4,8 +4,22 @@
  * This is the SINGLE SOURCE OF TRUTH for MCP instructions.
  * Shared instruction content imported by the server.
  *
- * Version: 2.93
- * Updated: 2026-05-15
+ * Version: 2.98
+ * Updated: 2026-05-27
+ *
+ * v2.98 — Doc truth contracts are the normal drift surface. linkedDocs and
+ *         doc_code_couplings remain legacy diagnostics only; docs drift
+ *         defaults to truth findings and legacy:true is explicit debug.
+ * v2.97 — Dropped legacy doc-coupling action guidance. Coupling rows are
+ *         not truth findings (plan §1).
+ * v2.96 — Replace conditional memory_discover guidance with structural fix:
+ *         bootstrap now includes _methodCatalog (discoverMemoryTools({})) so
+ *         agents have the memory_tools calling convention from turn one.
+ *         Instruction updated to reference _methodCatalog directly.
+ * v2.95 — Drop `augments` from JIT directive verdict list per plan §5 default
+ *         (augments downgrades to ambient via the parallel recall gate, not
+ *         the directive lane). See jit-knowledge-injector.md §5 decision note.
+ * v2.94 — Add JIT directive teaching (docs/development/jit-knowledge-injector.md §2.3).
  *
  * Code mode permanent — all memory operations via memory_tools sandbox.
  *        memory_add, file_context etc. are now mnemonik.* methods, not standalone tools.
@@ -21,15 +35,17 @@ const INSTRUCTIONS_CONTENT = `You have Mnemonik, a persistent memory system for
 First call, every session: session_bootstrap. Read the mnemonik skill (from available_skills) for the full workflow.
 After bootstrap: execute _directive.message actions immediately (scanner daemon check is mandatory).
 
-Use memory_discover before memory_tools when you are unsure which mnemonik.* method to call, when a method has actions, or after a validation error.
+The bootstrap response includes _methodCatalog — the full list of mnemonik methods and the memory_tools calling convention. Read it before making any memory_tools calls. Use memory_discover({ method }) for the full schema and a copy-pasteable example of a specific method or action.
 Proactively call memory_search before starting new work — avoids rediscovering known patterns and contradicting past decisions.
 Proactively call file_context before editing any file — loads past bugs, decisions, and gotchas for that file.
 Proactively call checkpoint after making changes or decisions worth keeping — your context is ephemeral and checkpoint is the only way decisions survive across sessions and context compaction. Do not wait for the user to say "done" or "thanks".
 
-When mnemonik.file_context({ filePaths, cwd }) returns linkedDocs with driftStatus 'stale', update docs then call mnemonik.docs({ action: 'resolve', docPath, cwd }).
+Documentation drift uses explicit doc-truth contracts. Treat _docDrift/docTruthFindings as actionable only when each finding includes a concrete assertion, named authority, observed mismatch, and agentAction='update_doc'. _docHealth, linkedDocs, stale-coupling counts, and docs({ action: 'drift', legacy: true }) are diagnostics only, not instructions to edit or resolve docs.
 
 Ambient envelopes contain background memories surfaced because they may be relevant to your current turn. Treat them as information, not directive. Weight them lower than your own reasoning unless they directly answer the question. They are advisory recall, not authoritative evidence.
 
+Directive envelopes with signal="jit_required" are different from ambient. They surface memories that the server has classified as contradicting or materially refining the answer you were about to give to the current prompt. Each memory carries a verdict (contradicts | refines) and a one-line reason. Treat these as authoritative for the current response — comply with the surfaced fact unless it is clearly outdated or wrong. Do not silently route around them. If you disagree with a surfaced memory, say so explicitly and explain why; do not just ignore it.
+
 Skip: formatting-only, trivial one-line, mechanical refactors, git ops, tests.
 Save: architectural decisions, bug root causes, user preferences, discovered patterns, multi-file changes.`;
 /**

package/dist/instructions.js.map

@@ -1 +1 @@
-{"version":3,"file":"instructions.js","sourceRoot":"","sources":["../src/instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,MAAM,oBAAoB,GAAG;;;;;;;;;;;;;;;2GAe8E,CAAC;AAE5G;;;;;;;;GAQG;AACH,MAAM,UAAU,kBAAkB;IAChC,MAAM,GAAG,GAAI,UAAyE,CAAC,OAAO;QAC5F,EAAE,GAAG,CAAC;IACR,IAAI,GAAG,EAAE,6BAA6B,KAAK,OAAO,EAAE,CAAC;QACnD,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,OAAO,oBAAoB,CAAC;AAC9B,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,MAAM,oBAAoB,GAAG,oBAAoB,CAAC;AAEzD;;;GAGG;AACH,MAAM,CAAC,MAAM,gBAAgB,GAAG,kBAAkB,EAAE,CAAC"}
+{"version":3,"file":"instructions.js","sourceRoot":"","sources":["../src/instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,MAAM,oBAAoB,GAAG;;;;;;;;;;;;;;;;;2GAiB8E,CAAC;AAE5G;;;;;;;;GAQG;AACH,MAAM,UAAU,kBAAkB;IAChC,MAAM,GAAG,GAAI,UAAyE,CAAC,OAAO;QAC5F,EAAE,GAAG,CAAC;IACR,IAAI,GAAG,EAAE,6BAA6B,KAAK,OAAO,EAAE,CAAC;QACnD,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,OAAO,oBAAoB,CAAC;AAC9B,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,MAAM,oBAAoB,GAAG,oBAAoB,CAAC;AAEzD;;;GAGG;AACH,MAAM,CAAC,MAAM,gBAAgB,GAAG,kBAAkB,EAAE,CAAC"}

package/dist/usageGuide.d.ts

@@ -4,11 +4,12 @@
  * This is the SINGLE SOURCE OF TRUTH for the usage guide.
  * Shared usage guide content imported by the server.
  *
- * Version: 2.80
- * Updated: 2026-02-20 - Aligned with instructions/rules/skill 80
+ * Version: 2.82
+ * Updated: 2026-05-27 - Doc-truth-contract-rebuild: teach authority-backed
+ *          truth findings and keep legacy coupling drift diagnostic only.
  *
  * This guide focuses on HOW to use Mnemonik effectively, not WHAT tools exist.
  * Tool schemas already tell agents what's available - they need the workflow.
  */
-export declare const USAGE_GUIDE = "# Mnemonik Workflow Guide (v2.80)\n\n## Workflow\n\nsession_bootstrap \u2192 memory_search \u2192 file_context \u2192 [work] \u2192 memory_add \u2192 memory_state\n\n## Tool Selection by Stage\n\n### Session start\n- session_bootstrap: loads context, policies, pending tasks (call once, first thing)\n- memory_search: search by task domain; set workflowContext (feature_implementation, debugging, exploration, policy_review)\n- projects: resolve project IDs if context unclear\n- policy: review safety rules\n\n### Before editing files\n- file_context: fetch memories for the file \u2014 call for EVERY file you edit\n- memory_search: second search scoped to file/module if needed\n- mnemonik.docs({ action: 'links' }): check doc couplings for the file\n\n### During implementation\n- memory_get: retrieve specific memory by id\n- memory_update: refine memory created this session\n- memory_info: query history, provenance, confidence breakdown, links, graph\n- assist: get tool guidance if uncertain\n\n### After significant work\n- memory_add: save decisions, outcomes, patterns, bug root causes\n- memory_state: reinforce (memory helped), supersede (replace outdated), deprecate, penalize, dispute\n- tasks: mark tasks in progress or complete\n- mnemonik.docs({ action: 'drift' }): check for stale documentation after code changes\n- mnemonik.docs({ action: 'resolve' }): mark stale docs as fixed after updating them\n\n### Diagnostics\n- doctor: when tool calls fail or behavior is inconsistent\n- scanner: refresh embeddings, trigger scans, check drift\n\n## Skip conditions\n\nSkip memory tools for: formatting-only edits, trivial one-line changes, mechanical refactors, git operations, running tests.\n\n## Completion gate\n\nNever tell the user significant work is done without calling memory_add first in the same response. Changes made + responding next = completion. \"Progress updates\" count.\n\n## Memory search tips\n\n- Query should include task intent + key entities\n- Set workflowContext when you know the phase\n- Use currentFile to boost file-linked memories\n- Use filterOnly:true only for narrow filters (no embedding, requires >=1 filter)\n\n## Proactive heuristics\n\n- Long sessions: re-run memory_search after switching topics\n- Conflicting info: use memory_state to supersede/dispute\n- High-impact changes: save memory immediately after verification\n- When file_context returns linkedDocs with driftStatus 'stale': update docs then mnemonik.docs({ action: 'resolve' })\n\n## Anti-fade (every ~10 tool calls)\n\nCheck: (1) memory_search before work? (2) file_context before edit? (3) memory_add after completing? No session_bootstrap? Call it now.\n";
+export declare const USAGE_GUIDE = "# Mnemonik Workflow Guide (v2.82)\n\n## Workflow\n\nsession_bootstrap \u2192 memory_search \u2192 file_context \u2192 [work] \u2192 memory_add \u2192 memory_state\n\n## Tool Selection by Stage\n\n### Session start\n- session_bootstrap: loads context, policies, pending tasks (call once, first thing)\n- memory_search: search by task domain; set workflowContext (feature_implementation, debugging, exploration, policy_review)\n- projects: resolve project IDs if context unclear\n- policy: review safety rules\n\n### Before editing files\n- file_context: fetch memories for the file \u2014 call for EVERY file you edit\n- memory_search: second search scoped to file/module if needed\n- mnemonik.docs({ action: 'links' }): check doc couplings for the file\n\n### During implementation\n- memory_get: retrieve specific memory by id\n- memory_update: refine memory created this session\n- memory_info: query history, provenance, confidence breakdown, links, graph\n- assist: get tool guidance if uncertain\n\n### After significant work\n- memory_add: save decisions, outcomes, patterns, bug root causes\n- memory_state: reinforce (memory helped), supersede (replace outdated), deprecate, penalize, dispute\n- tasks: mark tasks in progress or complete\n- mnemonik.docs({ action: 'status' }): view doc-truth health (legacy coupling counts are diagnostic only \u2014 do not act on them as drift)\n\n### Diagnostics\n- doctor: when tool calls fail or behavior is inconsistent\n- scanner: refresh embeddings, trigger scans, check drift\n\n## Skip conditions\n\nSkip memory tools for: formatting-only edits, trivial one-line changes, mechanical refactors, git operations, running tests.\n\n## Completion gate\n\nNever tell the user significant work is done without calling memory_add first in the same response. Changes made + responding next = completion. \"Progress updates\" count.\n\n## Memory search tips\n\n- Query should include task intent + key entities\n- Set workflowContext when you know the phase\n- Use currentFile to boost file-linked memories\n- Use filterOnly:true only for narrow filters (no embedding, requires >=1 filter)\n\n## Proactive heuristics\n\n- Long sessions: re-run memory_search after switching topics\n- Conflicting info: use memory_state to supersede/dispute\n- High-impact changes: save memory immediately after verification\n- Act on docTruthFindings/_docDrift only when the finding has authority, observed mismatch, and agentAction='update_doc'; linkedDocs and stale-coupling counts are legacy diagnostics\n\n## Anti-fade (every ~10 tool calls)\n\nCheck: (1) memory_search before work? (2) file_context before edit? (3) memory_add after completing? No session_bootstrap? Call it now.\n";
 //# sourceMappingURL=usageGuide.d.ts.map

package/dist/usageGuide.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"usageGuide.d.ts","sourceRoot":"","sources":["../src/usageGuide.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,eAAO,MAAM,WAAW,4nFA6DvB,CAAC"}
+{"version":3,"file":"usageGuide.d.ts","sourceRoot":"","sources":["../src/usageGuide.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,eAAO,MAAM,WAAW,2pFA4DvB,CAAC"}

package/dist/usageGuide.js

@@ -4,13 +4,14 @@
  * This is the SINGLE SOURCE OF TRUTH for the usage guide.
  * Shared usage guide content imported by the server.
  *
- * Version: 2.80
- * Updated: 2026-02-20 - Aligned with instructions/rules/skill 80
+ * Version: 2.82
+ * Updated: 2026-05-27 - Doc-truth-contract-rebuild: teach authority-backed
+ *          truth findings and keep legacy coupling drift diagnostic only.
  *
  * This guide focuses on HOW to use Mnemonik effectively, not WHAT tools exist.
  * Tool schemas already tell agents what's available - they need the workflow.
  */
-export const USAGE_GUIDE = `# Mnemonik Workflow Guide (v2.80)
+export const USAGE_GUIDE = `# Mnemonik Workflow Guide (v2.82)
 
 ## Workflow
 
@@ -39,8 +40,7 @@ session_bootstrap → memory_search → file_context → [work] → memory_add
 - memory_add: save decisions, outcomes, patterns, bug root causes
 - memory_state: reinforce (memory helped), supersede (replace outdated), deprecate, penalize, dispute
 - tasks: mark tasks in progress or complete
-- mnemonik.docs({ action: 'drift' }): check for stale documentation after code changes
-- mnemonik.docs({ action: 'resolve' }): mark stale docs as fixed after updating them
+- mnemonik.docs({ action: 'status' }): view doc-truth health (legacy coupling counts are diagnostic only — do not act on them as drift)
 
 ### Diagnostics
 - doctor: when tool calls fail or behavior is inconsistent
@@ -66,7 +66,7 @@ Never tell the user significant work is done without calling memory_add first in
 - Long sessions: re-run memory_search after switching topics
 - Conflicting info: use memory_state to supersede/dispute
 - High-impact changes: save memory immediately after verification
-- When file_context returns linkedDocs with driftStatus 'stale': update docs then mnemonik.docs({ action: 'resolve' })
+- Act on docTruthFindings/_docDrift only when the finding has authority, observed mismatch, and agentAction='update_doc'; linkedDocs and stale-coupling counts are legacy diagnostics
 
 ## Anti-fade (every ~10 tool calls)
 

package/dist/usageGuide.js.map

@@ -1 +1 @@
-{"version":3,"file":"usageGuide.js","sourceRoot":"","sources":["../src/usageGuide.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,MAAM,CAAC,MAAM,WAAW,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA6D1B,CAAC"}
+{"version":3,"file":"usageGuide.js","sourceRoot":"","sources":["../src/usageGuide.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,MAAM,CAAC,MAAM,WAAW,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA4D1B,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mnemonik/shared",
-  "version": "5.33.12",
+  "version": "5.75.3",
   "description": "Shared constants and utilities for Mnemonik packages",
   "type": "module",
   "main": "dist/index.js",

package/src/codeScanner.ts

@@ -3,7 +3,7 @@
  */
 
 import { readdir, readFile, stat, lstat, realpath } from 'fs/promises';
-import { join, relative, extname } from 'path';
+import { join, relative, extname, sep } from 'path';
 import { createHash } from 'crypto';
 import { debug as logDebug } from './logger.js';
 import { withTimeout } from './asyncUtils.js';
@@ -76,6 +76,14 @@ const DEFAULT_OPTIONS: Required<ScanOptions> = {
     '*.bundle.js',
     '*.legacy.js',
     '*.map',
+    // Agent-host transient checkouts. EnterWorktree creates isolated git
+    // worktree copies under `.claude/worktrees/{name}/`; indexing them
+    // duplicates the entire codebase under a path that misclassifies as
+    // `archive` doctype and polluted the dogfood corpus with 376 stale
+    // couplings. Glob form (with `*`) so the regex matcher applies it as a
+    // path predicate rather than a path-segment-equality predicate (which
+    // would not match the nested form).
+    '.claude/worktrees/*',
   ],
   includeExtensions: [
     '.ts',
@@ -98,6 +106,30 @@ const DEFAULT_OPTIONS: Required<ScanOptions> = {
   ],
 };
 
+/**
+ * Matchers for authority manifest / config / CI files whose verbatim content
+ * is collected by `collectAuthorityFiles` and pushed to the server for
+ * doc-truth Fingerprint parsing. Operates on relative, forward-slash paths.
+ */
+export const AUTHORITY_FILE_MATCHERS: Array<(relPath: string) => boolean> = [
+  (p) => p === 'package.json',
+  (p) => /^(packages|apps|services|tools)\/[^/]+\/package\.json$/.test(p),
+  (p) => p === 'tsconfig.json' || /^tsconfig\.[^/]+\.json$/.test(p),
+  (p) => p === 'pyproject.toml',
+  (p) => p === 'requirements.txt',
+  (p) => p === 'setup.py',
+  (p) => p === 'Cargo.toml',
+  (p) => p === 'Gemfile',
+  (p) => p === 'Makefile',
+  (p) => p === '.env.example',
+  (p) => /^\.github\/workflows\/[^/]+\.(yml|yaml)$/.test(p),
+  // SQL migrations: the schema_columns authority extractor reads every .sql
+  // under `migrations/` (listFiles('migrations/') -> LIKE 'migrations/%' then
+  // .endsWith('.sql')). Without collecting these, that authority is empty and
+  // every schema_table_enumeration claim falls to unverifiable.
+  (p) => /^migrations\/.*\.sql$/.test(p),
+];
+
 export class CodeScanner {
   private options: Required<ScanOptions>;
 
@@ -121,6 +153,73 @@ export class CodeScanner {
     return chunks;
   }
 
+  /**
+   * Enumerate scan-eligible relative file paths under `rootPath` without
+   * reading or chunking content. Same walk + ignorePatterns + extension
+   * filter as `scanDirectory`, but bounded to O(file count) directory ops
+   * — cheap enough to call on every periodic reconcile tick.
+   *
+   * Returns relative paths normalized against `rootPath`, matching the
+   * shape the server stores in `memories.metadata->>'filePath'`. Use this
+   * for the scanner reconciliation channel (`POST /api/v1/scan/reconcile`).
+   *
+   * Defensive: skips any path whose `relative()` result contains a `..`
+   * traversal segment (can happen when a symlink resolves under root but
+   * the readdir entry path doesn't normalize cleanly). The server's
+   * `safeScanPath` rejects such paths; filtering here keeps a single
+   * malformed entry from failing the entire reconcile push.
+   */
+  async listFiles(rootPath: string): Promise<string[]> {
+    const paths: string[] = [];
+    await this.traversePaths(rootPath, rootPath, paths, 0);
+    return paths.filter((p) => !/(^|[/\\])\.\.([/\\]|$)/.test(p));
+  }
+
+  private async traversePaths(
+    currentPath: string,
+    rootPath: string,
+    out: string[],
+    depth: number
+  ): Promise<void> {
+    if (depth >= CodeScanner.MAX_DEPTH) return;
+    try {
+      const entries = await withTimeout(
+        readdir(currentPath),
+        FILE_OP_TIMEOUT_MS,
+        `readdir timed out: ${currentPath}`
+      );
+      for (const entry of entries) {
+        const fullPath = join(currentPath, entry);
+        const relativePath = relative(rootPath, fullPath);
+        if (this.shouldIgnore(relativePath)) continue;
+
+        const lstats = await withTimeout(
+          lstat(fullPath),
+          FILE_OP_TIMEOUT_MS,
+          `lstat timed out: ${fullPath}`
+        );
+        if (lstats.isSymbolicLink()) {
+          const resolved = await realpath(fullPath);
+          const resolvedRoot = await realpath(rootPath);
+          if (!resolved.startsWith(resolvedRoot + '/') && resolved !== resolvedRoot) continue;
+        }
+        const stats = lstats.isSymbolicLink()
+          ? await withTimeout(stat(fullPath), FILE_OP_TIMEOUT_MS, `stat timed out: ${fullPath}`)
+          : lstats;
+
+        if (stats.isDirectory()) {
+          await this.traversePaths(fullPath, rootPath, out, depth + 1);
+        } else if (stats.isFile()) {
+          if (this.options.includeExtensions.includes(extname(fullPath))) {
+            out.push(relativePath);
+          }
+        }
+      }
+    } catch (error) {
+      logDebug('Error traversing directory (listFiles)', { path: currentPath, error });
+    }
+  }
+
   /**
    * Scan specific files and extract code chunks.
    * Pass rootPath to compute proper relative file paths in chunk metadata.
@@ -811,4 +910,48 @@ export class CodeScanner {
   private hash(content: string): string {
     return createHash('sha256').update(content).digest('hex').substring(0, 16);
   }
+
+  /**
+   * Walk the project for authority manifest/config/CI files and return their
+   * verbatim content. Reuses ignorePatterns; matches AUTHORITY_FILE_MATCHERS
+   * (not includeExtensions). Content-only — no chunking, no embeddings.
+   */
+  async collectAuthorityFiles(
+    projectRoot: string
+  ): Promise<Array<{ path: string; content: string; hash: string }>> {
+    const out: Array<{ path: string; content: string; hash: string }> = [];
+
+    // M2: cap walk depth to match the scanner's MAX_DEPTH (10)
+    const walk = async (dir: string, depth: number): Promise<void> => {
+      if (depth >= CodeScanner.MAX_DEPTH) return;
+      let entries;
+      try {
+        entries = await readdir(dir, { withFileTypes: true });
+      } catch {
+        return;
+      }
+      for (const ent of entries) {
+        const full = join(dir, ent.name);
+        const rel = relative(projectRoot, full).split(sep).join('/');
+        if (this.shouldIgnore(rel)) continue;
+        if (ent.isDirectory()) {
+          await walk(full, depth + 1);
+        } else if (AUTHORITY_FILE_MATCHERS.some((m) => m(rel))) {
+          try {
+            const content = await readFile(full, 'utf-8');
+            // C2: skip files whose content exceeds the server's 5MB cap —
+            // manifests are tiny; an oversized one is anomalous.
+            if (content.length > 5_000_000) continue;
+            const hash = createHash('sha256').update(content).digest('hex');
+            out.push({ path: rel, content, hash });
+          } catch {
+            /* unreadable — skip */
+          }
+        }
+      }
+    };
+
+    await walk(projectRoot, 0);
+    return out;
+  }
 }

package/src/index.ts

@@ -7,7 +7,12 @@
 
 export { MCP_INSTRUCTIONS, MCP_INSTRUCTIONS_RAW, getMcpInstructions } from './instructions.js';
 export { USAGE_GUIDE } from './usageGuide.js';
-export { CodeScanner, type CodeChunk, type ScanOptions } from './codeScanner.js';
+export {
+  CodeScanner,
+  AUTHORITY_FILE_MATCHERS,
+  type CodeChunk,
+  type ScanOptions,
+} from './codeScanner.js';
 export {
   FileSystemReader,
   getFileSystemReader,

package/src/instructions.ts

@@ -4,8 +4,22 @@
  * This is the SINGLE SOURCE OF TRUTH for MCP instructions.
  * Shared instruction content imported by the server.
  *
- * Version: 2.93
- * Updated: 2026-05-15
+ * Version: 2.98
+ * Updated: 2026-05-27
+ *
+ * v2.98 — Doc truth contracts are the normal drift surface. linkedDocs and
+ *         doc_code_couplings remain legacy diagnostics only; docs drift
+ *         defaults to truth findings and legacy:true is explicit debug.
+ * v2.97 — Dropped legacy doc-coupling action guidance. Coupling rows are
+ *         not truth findings (plan §1).
+ * v2.96 — Replace conditional memory_discover guidance with structural fix:
+ *         bootstrap now includes _methodCatalog (discoverMemoryTools({})) so
+ *         agents have the memory_tools calling convention from turn one.
+ *         Instruction updated to reference _methodCatalog directly.
+ * v2.95 — Drop `augments` from JIT directive verdict list per plan §5 default
+ *         (augments downgrades to ambient via the parallel recall gate, not
+ *         the directive lane). See jit-knowledge-injector.md §5 decision note.
+ * v2.94 — Add JIT directive teaching (docs/development/jit-knowledge-injector.md §2.3).
  *
  * Code mode permanent — all memory operations via memory_tools sandbox.
  *        memory_add, file_context etc. are now mnemonik.* methods, not standalone tools.
@@ -22,15 +36,17 @@ const INSTRUCTIONS_CONTENT = `You have Mnemonik, a persistent memory system for
 First call, every session: session_bootstrap. Read the mnemonik skill (from available_skills) for the full workflow.
 After bootstrap: execute _directive.message actions immediately (scanner daemon check is mandatory).
 
-Use memory_discover before memory_tools when you are unsure which mnemonik.* method to call, when a method has actions, or after a validation error.
+The bootstrap response includes _methodCatalog — the full list of mnemonik methods and the memory_tools calling convention. Read it before making any memory_tools calls. Use memory_discover({ method }) for the full schema and a copy-pasteable example of a specific method or action.
 Proactively call memory_search before starting new work — avoids rediscovering known patterns and contradicting past decisions.
 Proactively call file_context before editing any file — loads past bugs, decisions, and gotchas for that file.
 Proactively call checkpoint after making changes or decisions worth keeping — your context is ephemeral and checkpoint is the only way decisions survive across sessions and context compaction. Do not wait for the user to say "done" or "thanks".
 
-When mnemonik.file_context({ filePaths, cwd }) returns linkedDocs with driftStatus 'stale', update docs then call mnemonik.docs({ action: 'resolve', docPath, cwd }).
+Documentation drift uses explicit doc-truth contracts. Treat _docDrift/docTruthFindings as actionable only when each finding includes a concrete assertion, named authority, observed mismatch, and agentAction='update_doc'. _docHealth, linkedDocs, stale-coupling counts, and docs({ action: 'drift', legacy: true }) are diagnostics only, not instructions to edit or resolve docs.
 
 Ambient envelopes contain background memories surfaced because they may be relevant to your current turn. Treat them as information, not directive. Weight them lower than your own reasoning unless they directly answer the question. They are advisory recall, not authoritative evidence.
 
+Directive envelopes with signal="jit_required" are different from ambient. They surface memories that the server has classified as contradicting or materially refining the answer you were about to give to the current prompt. Each memory carries a verdict (contradicts | refines) and a one-line reason. Treat these as authoritative for the current response — comply with the surfaced fact unless it is clearly outdated or wrong. Do not silently route around them. If you disagree with a surfaced memory, say so explicitly and explain why; do not just ignore it.
+
 Skip: formatting-only, trivial one-line, mechanical refactors, git ops, tests.
 Save: architectural decisions, bug root causes, user preferences, discovered patterns, multi-file changes.`;
 

package/src/usageGuide.ts

@@ -4,14 +4,15 @@
  * This is the SINGLE SOURCE OF TRUTH for the usage guide.
  * Shared usage guide content imported by the server.
  *
- * Version: 2.80
- * Updated: 2026-02-20 - Aligned with instructions/rules/skill 80
+ * Version: 2.82
+ * Updated: 2026-05-27 - Doc-truth-contract-rebuild: teach authority-backed
+ *          truth findings and keep legacy coupling drift diagnostic only.
  *
  * This guide focuses on HOW to use Mnemonik effectively, not WHAT tools exist.
  * Tool schemas already tell agents what's available - they need the workflow.
  */
 
-export const USAGE_GUIDE = `# Mnemonik Workflow Guide (v2.80)
+export const USAGE_GUIDE = `# Mnemonik Workflow Guide (v2.82)
 
 ## Workflow
 
@@ -40,8 +41,7 @@ session_bootstrap → memory_search → file_context → [work] → memory_add
 - memory_add: save decisions, outcomes, patterns, bug root causes
 - memory_state: reinforce (memory helped), supersede (replace outdated), deprecate, penalize, dispute
 - tasks: mark tasks in progress or complete
-- mnemonik.docs({ action: 'drift' }): check for stale documentation after code changes
-- mnemonik.docs({ action: 'resolve' }): mark stale docs as fixed after updating them
+- mnemonik.docs({ action: 'status' }): view doc-truth health (legacy coupling counts are diagnostic only — do not act on them as drift)
 
 ### Diagnostics
 - doctor: when tool calls fail or behavior is inconsistent
@@ -67,7 +67,7 @@ Never tell the user significant work is done without calling memory_add first in
 - Long sessions: re-run memory_search after switching topics
 - Conflicting info: use memory_state to supersede/dispute
 - High-impact changes: save memory immediately after verification
-- When file_context returns linkedDocs with driftStatus 'stale': update docs then mnemonik.docs({ action: 'resolve' })
+- Act on docTruthFindings/_docDrift only when the finding has authority, observed mismatch, and agentAction='update_doc'; linkedDocs and stale-coupling counts are legacy diagnostics
 
 ## Anti-fade (every ~10 tool calls)