@monoes/monograph 1.5.7 → 1.5.8

package/README.md

@@ -88,13 +88,13 @@ Monograph utilizes a dual-tier parsing strategy for extracting code structure an
 
 1. **Tree-sitter AST Parsers (25 supported extensions)**:
    - **Extensions**: `.ts`, `.tsx`, `.js`, `.jsx`, `.mjs`, `.cjs`, `.py`, `.go`, `.rs`, `.java`, `.c`, `.h`, `.cpp`, `.cc`, `.cxx`, `.hpp`, `.hxx`, `.cs`, `.rb`, `.swift`, `.php`, `.vue`, `.kt`, `.kts`, `.dart`.
-   - **Grammar Loader**: Dynamically loads and caches Tree-sitter grammars per extension via `getParser(ext)` ([`loader.ts:64-83`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/parsers/loader.ts#L64-L83)). Supports `<script>` block isolation for `.vue` files ([`loader.ts:128-142`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/parsers/loader.ts#L128-L142)).
+   - **Grammar Loader**: Dynamically loads and caches Tree-sitter grammars per extension via `getParser(ext)` ([`loader.ts:64-83`](packages/@monomind/monograph/src/parsers/loader.ts#L64-L83)). Supports `<script>` block isolation for `.vue` files ([`loader.ts:128-142`](packages/@monomind/monograph/src/parsers/loader.ts#L128-L142)).
 2. **Regex Fallback Parsers (5 languages)**:
-   - Lightweight regex-based symbol extractors for languages when Tree-sitter grammars are uninstalled or unsupported: **Scala**, **Lua**, **Zig**, **PowerShell**, and **Elixir** ([`language-parsers.ts:1-100`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/parsers/language-parsers.ts#L1-L100)).
+   - Lightweight regex-based symbol extractors for languages when Tree-sitter grammars are uninstalled or unsupported: **Scala**, **Lua**, **Zig**, **PowerShell**, and **Elixir** ([`language-parsers.ts:1-100`](packages/@monomind/monograph/src/parsers/language-parsers.ts#L1-L100)).
 
 ## SQLite Database Schema
 
-The graph is stored in a WAL-mode SQLite database (`PRAGMA journal_mode = WAL`) managed in [`schema.ts`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/storage/schema.ts) and [`db.ts`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/storage/db.ts):
+The graph is stored in a WAL-mode SQLite database (`PRAGMA journal_mode = WAL`) managed in [`schema.ts`](packages/@monomind/monograph/src/storage/schema.ts) and [`db.ts`](packages/@monomind/monograph/src/storage/db.ts):
 
 - **`nodes`**: Code symbols and files (`id`, `label`, `name`, `norm_label`, `file_path`, `start_line`, `end_line`, `community_id`, `is_exported`, `language`, `properties`, `embedding`).
 - **`edges`**: Directed relationships between nodes (`id`, `source_id`, `target_id`, `relation`, `confidence`, `confidence_score`, `weight`, `reason`, `evidence`).
@@ -105,7 +105,7 @@ The graph is stored in a WAL-mode SQLite database (`PRAGMA journal_mode = WAL`)
 
 ## Relationship Types
 
-Monograph defines typed edges ([`types.ts:20-29`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/types.ts#L20-L29)) categorized into structural, static analysis, and semantic relationships:
+Monograph defines typed edges ([`types.ts:20-29`](packages/@monomind/monograph/src/types.ts#L20-L29)) categorized into structural, static analysis, and semantic relationships:
 
 - **`CONTAINS`**: Parent container to child element (e.g. File contains Class/Function, Class contains Method).
 - **`IMPORTS`**: File/Module import dependency (`import { x } from './y'`).
@@ -115,7 +115,7 @@ Monograph defines typed edges ([`types.ts:20-29`](file:///Users/morteza/Desktop/
 
 ## Blast Radius Calculation (`rippleImpact`)
 
-Monograph calculates downstream cascade impact using the multi-hop `rippleImpact` BFS algorithm ([`ripple-impact.ts:51-84`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/graph/ripple-impact.ts#L51-L84)):
+Monograph calculates downstream cascade impact using the multi-hop `rippleImpact` BFS algorithm ([`ripple-impact.ts:51-84`](packages/@monomind/monograph/src/graph/ripple-impact.ts#L51-L84)):
 
 - **Algorithm**: Breadth-First Search propagating through outgoing directed edge adjacency maps.
 - **Scoring Formula**:
@@ -125,7 +125,7 @@ Monograph calculates downstream cascade impact using the multi-hop `rippleImpact
 
 ## Graph Freshness & Git Staleness Tracking
 
-Monograph maintains graph synchronization with git repository state without full re-indexes ([`git-staleness.ts:13-66`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/staleness/git-staleness.ts#L13-L66)):
+Monograph maintains graph synchronization with git repository state without full re-indexes ([`git-staleness.ts:13-66`](packages/@monomind/monograph/src/staleness/git-staleness.ts#L13-L66)):
 
 - **Commit Verification**: Compares stored `last_commit_hash` in `index_meta` against `git rev-parse HEAD`.
 - **Change Diffing**: If hashes diverge, executes `git diff --name-only <indexedCommit>..HEAD` to populate `changedSince` files.
@@ -134,10 +134,10 @@ Monograph maintains graph synchronization with git repository state without full
 
 ### Incremental Watch Mode
 
-`monomind monograph watch` (and the `monograph_watch` MCP tool) debounces file changes by 3s ([`watcher.ts:108-110`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/watch/watcher.ts#L108-L110)), then updates the graph per changed file — delete existing nodes/edges for that file, re-parse, re-insert ([`orchestrator.ts:312-365`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/pipeline/orchestrator.ts#L312-L365)):
+`monomind monograph watch` (and the `monograph_watch` MCP tool) debounces file changes by 3s ([`watcher.ts:108-110`](packages/@monomind/monograph/src/watch/watcher.ts#L108-L110)), then updates the graph per changed file — delete existing nodes/edges for that file, re-parse, re-insert ([`orchestrator.ts:312-365`](packages/@monomind/monograph/src/pipeline/orchestrator.ts#L312-L365)):
 
-- **Incremental Threshold**: If a batch exceeds `INCREMENTAL_THRESHOLD` (20 changed files), it falls back to a full rebuild instead of per-file updates ([`orchestrator.ts:269-279`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/pipeline/orchestrator.ts#L269-L279)).
-- **Deferred Full Rebuild**: After `FULL_REBUILD_IDLE_MS` (60s) with no further incremental activity, watch mode runs one full rebuild to refresh aggregate phases (communities, god-nodes, surprises, churn, report) that incremental updates don't recompute ([`watcher.ts:40-59`](file:///Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph/src/watch/watcher.ts#L40-L59)).
+- **Incremental Threshold**: If a batch exceeds `INCREMENTAL_THRESHOLD` (20 changed files), it falls back to a full rebuild instead of per-file updates ([`orchestrator.ts:269-279`](packages/@monomind/monograph/src/pipeline/orchestrator.ts#L269-L279)).
+- **Deferred Full Rebuild**: After `FULL_REBUILD_IDLE_MS` (60s) with no further incremental activity, watch mode runs one full rebuild to refresh aggregate phases (communities, god-nodes, surprises, churn, report) that incremental updates don't recompute ([`watcher.ts:40-59`](packages/@monomind/monograph/src/watch/watcher.ts#L40-L59)).
 
 ## Links
 

package/dist/src/analysis/changed-files.d.ts

@@ -2,6 +2,9 @@ export declare class ChangedFilesError extends Error {
     readonly kind: 'invalid_ref' | 'git_failed' | 'parse_error';
     constructor(message: string, kind: 'invalid_ref' | 'git_failed' | 'parse_error');
 }
+/** @deprecated use git-ref.js's validateGitRef directly for new code — kept
+ *  here so existing importers of this module's validateGitRef keep getting
+ *  a typed ChangedFilesError('invalid_ref') instead of InvalidGitRefError. */
 export declare function validateGitRef(ref: string): string;
 export declare function getChangedFiles(root: string, sinceRef: string): Promise<Set<string>>;
 export declare function filterResultsByChangedFiles<T extends {

package/dist/src/analysis/changed-files.d.ts.map

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package/dist/src/analysis/changed-files.js

@@ -1,5 +1,6 @@
 import { execFileSync } from 'child_process';
 import * as path from 'path';
+import { validateGitRef as sharedValidateGitRef, InvalidGitRefError } from './git-ref.js';
 export class ChangedFilesError extends Error {
     kind;
     constructor(message, kind) {
@@ -8,18 +9,19 @@ export class ChangedFilesError extends Error {
         this.name = 'ChangedFilesError';
     }
 }
-// Leading '-' is rejected explicitly (not just by the character class) so a
-// value like "--output=/tmp/pwned" can't be passed through and interpreted
-// by git as a command-line option instead of a ref (git option injection).
-const VALID_REF_RE = /^[a-zA-Z0-9\-_./@~^]+$/;
+/** @deprecated use git-ref.js's validateGitRef directly for new code — kept
+ *  here so existing importers of this module's validateGitRef keep getting
+ *  a typed ChangedFilesError('invalid_ref') instead of InvalidGitRefError. */
 export function validateGitRef(ref) {
-    if (ref.startsWith('-')) {
-        throw new ChangedFilesError(`Invalid git ref: "${ref}". Refs must not start with '-' (would be interpreted as a git option)`, 'invalid_ref');
+    try {
+        return sharedValidateGitRef(ref);
     }
-    if (VALID_REF_RE.test(ref)) {
-        return ref;
+    catch (err) {
+        if (err instanceof InvalidGitRefError) {
+            throw new ChangedFilesError(err.message, 'invalid_ref');
+        }
+        throw err;
     }
-    throw new ChangedFilesError(`Invalid git ref: "${ref}". Must match ${VALID_REF_RE.source}`, 'invalid_ref');
 }
 export async function getChangedFiles(root, sinceRef) {
     validateGitRef(sinceRef);

package/dist/src/analysis/changed-files.js.map

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package/dist/src/analysis/changed-workspaces.d.ts.map

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package/dist/src/analysis/changed-workspaces.js

@@ -1,6 +1,7 @@
 import { execFileSync } from 'child_process';
 import { existsSync, readdirSync, readFileSync } from 'fs';
 import { join, relative, resolve } from 'path';
+import { validateGitRef } from './git-ref.js';
 function findWorkspaceRoots(projectRoot) {
     // Detect pnpm/npm/yarn workspaces
     let pkg;
@@ -38,15 +39,7 @@ function findWorkspaceRoots(projectRoot) {
     return roots;
 }
 export function getChangedWorkspaces(projectRoot, sinceRef, workspaceRoots) {
-    // Validate git ref (same allowlist as changed-files.ts). Leading '-' is
-    // rejected explicitly so a value like "--output=/tmp/pwned" can't be
-    // interpreted by git as a command-line option (git option injection).
-    if (sinceRef.startsWith('-')) {
-        throw new Error(`Invalid git ref: "${sinceRef}". Refs must not start with '-' (would be interpreted as a git option)`);
-    }
-    if (!/^[a-zA-Z0-9\-_./@~^]+$/.test(sinceRef)) {
-        throw new Error(`Invalid git ref: "${sinceRef}"`);
-    }
+    validateGitRef(sinceRef);
     let changedFiles;
     try {
         // execFileSync with array argv — no shell involved, so a `projectRoot`

package/dist/src/analysis/changed-workspaces.js.map

@@ -1 +1 @@
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package/dist/src/analysis/git-changed-files.d.ts

@@ -1,3 +1,6 @@
+/** @deprecated use git-ref.js's validateGitRef directly for new code. Kept
+ *  as a void-returning wrapper so existing call sites in this file don't
+ *  need to change shape. */
 export declare function validateGitRef(ref: string): void;
 export declare function resolveGitToplevel(cwd: string): string;
 export declare function collectGitPaths(root: string, since?: string): string[];

package/dist/src/analysis/git-changed-files.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"git-changed-files.d.ts","sourceRoot":"","sources":["../../../src/analysis/git-changed-files.ts"],"names":[],"mappings":"AAIA;;4BAE4B;AAC5B,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAEhD;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMtD;AAED,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAuBtE;AAED,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,IAAI,CAQhF;AAED,wBAAgB,2BAA2B,CAAC,CAAC,SAAS;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,EACxE,OAAO,EAAE,CAAC,EAAE,EACZ,YAAY,EAAE,MAAM,EAAE,GACrB,CAAC,EAAE,CAGL;AAED,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAG1E"}

package/dist/src/analysis/git-changed-files.js

@@ -1,15 +1,15 @@
-import { execSync } from 'node:child_process';
+import { execFileSync } from 'node:child_process';
 import * as path from 'node:path';
-const GIT_REF_ALLOWLIST = /^[a-zA-Z0-9._/~^@{}[\]:-]+$/;
-const DANGEROUS_PATTERNS = /\.\.|`|\$\(|;|&&|\|\|/;
+import { validateGitRef as sharedValidateGitRef } from './git-ref.js';
+/** @deprecated use git-ref.js's validateGitRef directly for new code. Kept
+ *  as a void-returning wrapper so existing call sites in this file don't
+ *  need to change shape. */
 export function validateGitRef(ref) {
-    if (!GIT_REF_ALLOWLIST.test(ref) || DANGEROUS_PATTERNS.test(ref)) {
-        throw new Error(`Invalid git ref: ${JSON.stringify(ref)} — only alphanumeric, dots, slashes, hyphens, and common git ref characters are allowed`);
-    }
+    sharedValidateGitRef(ref);
 }
 export function resolveGitToplevel(cwd) {
     try {
-        return execSync('git rev-parse --show-toplevel', { cwd, encoding: 'utf8' }).trim();
+        return execFileSync('git', ['rev-parse', '--show-toplevel'], { cwd, encoding: 'utf8' }).trim();
     }
     catch {
         return cwd;
@@ -17,15 +17,20 @@ export function resolveGitToplevel(cwd) {
 }
 export function collectGitPaths(root, since) {
     try {
-        let cmd;
+        // execFileSync with an array argv — no shell involved, so `since` and
+        // `root` cannot break out via `;`/`&&`/`$(...)` even without the
+        // DANGEROUS_PATTERNS deny-list this file used to rely on instead
+        // (the deny-list was also the only implementation among the four
+        // duplicated validators that rejected the common `main..HEAD` range).
+        let args;
         if (since) {
-            validateGitRef(since);
-            cmd = `git diff --name-only --diff-filter=ACM ${since}`;
+            sharedValidateGitRef(since);
+            args = ['diff', '--name-only', '--diff-filter=ACM', since];
         }
         else {
-            cmd = 'git ls-files';
+            args = ['ls-files'];
         }
-        const output = execSync(cmd, { cwd: root, encoding: 'utf8' });
+        const output = execFileSync('git', args, { cwd: root, encoding: 'utf8' });
         return output
             .split('\n')
             .map(l => l.trim())

package/dist/src/analysis/git-changed-files.js.map

@@ -1 +1 @@
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+{"version":3,"file":"git-changed-files.js","sourceRoot":"","sources":["../../../src/analysis/git-changed-files.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,cAAc,IAAI,oBAAoB,EAAE,MAAM,cAAc,CAAC;AAEtE;;4BAE4B;AAC5B,MAAM,UAAU,cAAc,CAAC,GAAW;IACxC,oBAAoB,CAAC,GAAG,CAAC,CAAC;AAC5B,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAW;IAC5C,IAAI,CAAC;QACH,OAAO,YAAY,CAAC,KAAK,EAAE,CAAC,WAAW,EAAE,iBAAiB,CAAC,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;IACjG,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAC;IACb,CAAC;AACH,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAY,EAAE,KAAc;IAC1D,IAAI,CAAC;QACH,sEAAsE;QACtE,iEAAiE;QACjE,iEAAiE;QACjE,iEAAiE;QACjE,sEAAsE;QACtE,IAAI,IAAc,CAAC;QACnB,IAAI,KAAK,EAAE,CAAC;YACV,oBAAoB,CAAC,KAAK,CAAC,CAAC;YAC5B,IAAI,GAAG,CAAC,MAAM,EAAE,aAAa,EAAE,mBAAmB,EAAE,KAAK,CAAC,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,IAAI,GAAG,CAAC,UAAU,CAAC,CAAC;QACtB,CAAC;QACD,MAAM,MAAM,GAAG,YAAY,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE,GAAG,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC;QAC1E,OAAO,MAAM;aACV,KAAK,CAAC,IAAI,CAAC;aACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;aAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;aACzB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IACrC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,CAAC;IACZ,CAAC;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,IAAY,EAAE,KAAc;IAC7D,IAAI,CAAC,KAAK;QAAE,OAAO,IAAI,CAAC;IACxB,IAAI,CAAC;QACH,cAAc,CAAC,KAAK,CAAC,CAAC;QACtB,OAAO,eAAe,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;IACtC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,MAAM,UAAU,2BAA2B,CACzC,OAAY,EACZ,YAAsB;IAEtB,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACrE,OAAO,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;AACzE,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAAY,EAAE,KAAa;IAC9D,cAAc,CAAC,KAAK,CAAC,CAAC;IACtB,OAAO,eAAe,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;AACtC,CAAC"}

package/dist/src/analysis/git-ref.d.ts

@@ -0,0 +1,33 @@
+/**
+ * Shared git-ref validator.
+ *
+ * Previously duplicated 4 ways (monovector/diff-classifier.ts in the CLI
+ * package, plus changed-files.ts, git-changed-files.ts, and
+ * changed-workspaces.ts here) and already disagreeing on `main..HEAD` /
+ * `main...HEAD` — a valid, extremely common git range. This is
+ * diff-classifier.ts's implementation (allowlist + leading-dash guard +
+ * explicit range carve-out + length cap), merged with changed-files.ts's
+ * typed `ChangedFilesError` for callers that want to distinguish an invalid
+ * ref from an actual git failure.
+ */
+export declare class InvalidGitRefError extends Error {
+    constructor(message: string);
+}
+/**
+ * Validate a git ref before it reaches a git invocation.
+ *
+ * - Rejects shell metacharacters via an allowlist (alphanumeric plus
+ *   `-._/~^@`).
+ * - Rejects a leading `-` explicitly: `execFile`/`execFileSync` with an
+ *   array argv defeats *shell* injection, but does not stop the `git`
+ *   binary itself from treating an attacker-controlled ref as a flag
+ *   (`--output=...`, `-G<regex>`, `-S<string>`).
+ * - Allows `..`/`...` ranges (`main..HEAD`, `main...HEAD`) — the primary,
+ *   extremely common case a naive "reject any `..`" rule breaks.
+ * - Caps length at 256.
+ *
+ * Throws `InvalidGitRefError` (not a plain `Error`) so callers can
+ * distinguish "bad input" from "git itself failed".
+ */
+export declare function validateGitRef(ref: string): string;
+//# sourceMappingURL=git-ref.d.ts.map

package/dist/src/analysis/git-ref.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"git-ref.d.ts","sourceRoot":"","sources":["../../../src/analysis/git-ref.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,qBAAa,kBAAmB,SAAQ,KAAK;IAC3C,YAAY,OAAO,EAAE,MAAM,EAG1B;CACF;AAID;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAiBlD"}

package/dist/src/analysis/git-ref.js

@@ -0,0 +1,54 @@
+/**
+ * Shared git-ref validator.
+ *
+ * Previously duplicated 4 ways (monovector/diff-classifier.ts in the CLI
+ * package, plus changed-files.ts, git-changed-files.ts, and
+ * changed-workspaces.ts here) and already disagreeing on `main..HEAD` /
+ * `main...HEAD` — a valid, extremely common git range. This is
+ * diff-classifier.ts's implementation (allowlist + leading-dash guard +
+ * explicit range carve-out + length cap), merged with changed-files.ts's
+ * typed `ChangedFilesError` for callers that want to distinguish an invalid
+ * ref from an actual git failure.
+ */
+export class InvalidGitRefError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = 'InvalidGitRefError';
+    }
+}
+const VALID_REF_RE = /^[a-zA-Z0-9_\-./~^@]+$/;
+/**
+ * Validate a git ref before it reaches a git invocation.
+ *
+ * - Rejects shell metacharacters via an allowlist (alphanumeric plus
+ *   `-._/~^@`).
+ * - Rejects a leading `-` explicitly: `execFile`/`execFileSync` with an
+ *   array argv defeats *shell* injection, but does not stop the `git`
+ *   binary itself from treating an attacker-controlled ref as a flag
+ *   (`--output=...`, `-G<regex>`, `-S<string>`).
+ * - Allows `..`/`...` ranges (`main..HEAD`, `main...HEAD`) — the primary,
+ *   extremely common case a naive "reject any `..`" rule breaks.
+ * - Caps length at 256.
+ *
+ * Throws `InvalidGitRefError` (not a plain `Error`) so callers can
+ * distinguish "bad input" from "git itself failed".
+ */
+export function validateGitRef(ref) {
+    if (!VALID_REF_RE.test(ref)) {
+        throw new InvalidGitRefError(`Invalid git ref: "${ref}" contains unsafe characters`);
+    }
+    if (ref.startsWith('-')) {
+        throw new InvalidGitRefError(`Invalid git ref: "${ref}" must not start with '-'`);
+    }
+    // Multiple dots are only valid as a two-dot or three-dot range between two
+    // otherwise-valid ref segments (main..HEAD, main...HEAD) — anything else
+    // containing ".." is a path-traversal-shaped pattern and rejected.
+    if (ref.includes('..') && !/^[a-zA-Z0-9_-]+\.\.\.?[a-zA-Z0-9_-]+$/.test(ref)) {
+        throw new InvalidGitRefError(`Invalid git ref: "${ref}" has a suspicious '..' pattern`);
+    }
+    if (ref.length > 256) {
+        throw new InvalidGitRefError(`Invalid git ref: "${ref}" is too long`);
+    }
+    return ref;
+}
+//# sourceMappingURL=git-ref.js.map

package/dist/src/analysis/git-ref.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"git-ref.js","sourceRoot":"","sources":["../../../src/analysis/git-ref.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,MAAM,OAAO,kBAAmB,SAAQ,KAAK;IAC3C,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,oBAAoB,CAAC;IACnC,CAAC;CACF;AAED,MAAM,YAAY,GAAG,wBAAwB,CAAC;AAE9C;;;;;;;;;;;;;;;GAeG;AACH,MAAM,UAAU,cAAc,CAAC,GAAW;IACxC,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QAC5B,MAAM,IAAI,kBAAkB,CAAC,qBAAqB,GAAG,8BAA8B,CAAC,CAAC;IACvF,CAAC;IACD,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,IAAI,kBAAkB,CAAC,qBAAqB,GAAG,2BAA2B,CAAC,CAAC;IACpF,CAAC;IACD,2EAA2E;IAC3E,yEAAyE;IACzE,mEAAmE;IACnE,IAAI,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QAC7E,MAAM,IAAI,kBAAkB,CAAC,qBAAqB,GAAG,iCAAiC,CAAC,CAAC;IAC1F,CAAC;IACD,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;QACrB,MAAM,IAAI,kBAAkB,CAAC,qBAAqB,GAAG,eAAe,CAAC,CAAC;IACxE,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC"}

package/dist/src/analyze/boundary-analysis.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"boundary-analysis.d.ts","sourceRoot":"","sources":["../../../src/analyze/boundary-analysis.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,8BAA8B,CAAC;AAE3E,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,KAAK,EAAE,uBAAuB,EAAE,MAAM,8BAA8B,CAAC;AAE5E,MAAM,WAAW,sBAAsB;IACrC,UAAU,EAAE,uBAAuB,EAAE,CAAC;IACtC,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,EAAE,MAAM,CAAC;CACxB;AAaD,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,UAAU,EAAE,EACrB,MAAM,EAAE,sBAAsB,GAC7B,uBAAuB,EAAE,CA6C3B;AAED,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,UAAU,EAAE,EACrB,MAAM,EAAE,sBAAsB,GAC7B,sBAAsB,CAoDxB"}
+{"version":3,"file":"boundary-analysis.d.ts","sourceRoot":"","sources":["../../../src/analyze/boundary-analysis.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,8BAA8B,CAAC;AAE3E,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,KAAK,EAAE,uBAAuB,EAAE,MAAM,8BAA8B,CAAC;AAE5E,MAAM,WAAW,sBAAsB;IACrC,UAAU,EAAE,uBAAuB,EAAE,CAAC;IACtC,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,EAAE,MAAM,CAAC;CACxB;AA0DD,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,UAAU,EAAE,EACrB,MAAM,EAAE,sBAAsB,GAC7B,uBAAuB,EAAE,CAE3B;AAED,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,UAAU,EAAE,EACrB,MAAM,EAAE,sBAAsB,GAC7B,sBAAsB,CAoDxB"}

package/dist/src/analyze/boundary-analysis.js

@@ -7,48 +7,48 @@ function isReachableOrEntry(mod) {
 function hasRules(config, zoneName) {
     return config.rules.some(r => r.from.name === zoneName);
 }
-export function findBoundaryViolations(modules, config) {
-    if (config.zones.length === 0)
-        return [];
-    const zoneCache = new Map();
-    const classify = (filePath) => {
-        if (zoneCache.has(filePath))
-            return zoneCache.get(filePath);
-        const zone = classifyZone(config, filePath);
-        zoneCache.set(filePath, zone);
-        return zone;
-    };
-    const filePathByPath = new Map(modules.map(m => [m.filePath, m]));
-    const violations = [];
-    for (const mod of modules) {
-        if (!isReachableOrEntry(mod))
-            continue;
-        const fromZone = classify(mod.filePath);
-        if (!fromZone)
+/**
+ * Every file `mod` reaches into another module through: barrel re-exports
+ * (`mod.reExports`) and, WHEN PRESENT, symbol references (`mod.references`,
+ * where `fromFile` is the file the imported symbol lives in — see
+ * graph/node-types.ts). `references` carries real line numbers; `reExports`
+ * does not, so those edges still report line 1.
+ *
+ * CAVEAT (found in review, kept here rather than silently reverted): the
+ * ONLY writer of `ModuleNode.references` anywhere in this package is
+ * graph/re-exports/propagate.ts's barrel-re-export propagation — a plain
+ * `import { x } from '../other-zone/y'` with no barrel/re-export anywhere in
+ * the chain never populates `references` at all, so this function does NOT
+ * actually catch that case despite reading as if it does. Fixing that
+ * properly means teaching some real import-graph builder to push a
+ * SymbolReference for every ordinary import, which nothing in this package
+ * currently does — `analyzeBoundaries`/`findBoundaryViolations` here (and
+ * their sibling `unused-exports.ts`) have zero production callers; both
+ * operate purely on hand-constructed ModuleNode fixtures in their own test
+ * files, not on any real parsed codebase. If you need working, wired-up
+ * boundary checking today, use `pipeline/phases/boundary.ts`'s
+ * `detectBoundaryViolations`, which queries the SQLite `edges` table
+ * directly and already covers every import edge, barrel or not.
+ */
+function edgesForModule(mod) {
+    const seen = new Set();
+    const edges = [];
+    for (const edge of mod.reExports) {
+        if (seen.has(edge.toFile))
             continue;
-        if (!hasRules(config, fromZone))
+        seen.add(edge.toFile);
+        edges.push({ toFile: edge.toFile, line: 1, col: 0 });
+    }
+    for (const ref of mod.references) {
+        if (seen.has(ref.fromFile))
             continue;
-        for (const edge of mod.reExports) {
-            const toPath = edge.toFile;
-            const toZone = classify(toPath);
-            if (!toZone)
-                continue;
-            if (fromZone === toZone)
-                continue;
-            if (!isImportAllowed(config, mod.filePath, toPath)) {
-                violations.push({
-                    fromPath: mod.filePath,
-                    toPath,
-                    fromZone,
-                    toZone,
-                    importSpecifier: toPath,
-                    line: 1,
-                    col: 0,
-                });
-            }
-        }
+        seen.add(ref.fromFile);
+        edges.push({ toFile: ref.fromFile, line: ref.line ?? 1, col: 0 });
     }
-    return violations;
+    return edges;
+}
+export function findBoundaryViolations(modules, config) {
+    return analyzeBoundaries(modules, config).violations;
 }
 export function analyzeBoundaries(modules, config) {
     if (config.zones.length === 0) {
@@ -75,7 +75,7 @@ export function analyzeBoundaries(modules, config) {
         }
         if (!hasRules(config, fromZone))
             continue;
-        for (const edge of mod.reExports) {
+        for (const edge of edgesForModule(mod)) {
             const toPath = edge.toFile;
             checkedEdges++;
             const toZone = classify(toPath);
@@ -90,8 +90,8 @@ export function analyzeBoundaries(modules, config) {
                     fromZone,
                     toZone,
                     importSpecifier: toPath,
-                    line: 1,
-                    col: 0,
+                    line: edge.line,
+                    col: edge.col,
                 });
             }
         }

package/dist/src/analyze/boundary-analysis.js.map

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

@@ -42,6 +42,7 @@ export * from './web/analyze-api.js';
 export * from './web/mcp-http.js';
 export * from './mcp-resources/index.js';
 export * from './analysis/shape-extractor.js';
+export * from './analysis/git-ref.js';
 export * from './mcp-tools/tool-map.js';
 export * from './mcp-tools/shape-check.js';
 export * from './mcp-tools/neighbors.js';

package/dist/src/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,yBAAyB,CAAC;AACxC,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AACpC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,mBAAmB,CAAC;AAClC,cAAc,qBAAqB,CAAC;AACpC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,kBAAkB,CAAC;AACjC,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,qBAAqB,CAAC;AACpC,cAAc,iBAAiB,CAAC;AAChC,cAAc,sBAAsB,CAAC;AACrC,cAAc,oBAAoB,CAAC;AACnC,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,iBAAiB,CAAC;AAChC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,wBAAwB,CAAC;AACvC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,2BAA2B,CAAC;AAC1C,cAAc,2BAA2B,CAAC;AAE1C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,iBAAiB,CAAC;AAChC,cAAc,cAAc,CAAC;AAC7B,cAAc,qBAAqB,CAAC;AACpC,cAAc,mBAAmB,CAAC;AAClC,cAAc,sBAAsB,CAAC;AACrC,cAAc,mBAAmB,CAAC;AAClC,cAAc,0BAA0B,CAAC;AACzC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,uBAAuB,CAAC;AACtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,wBAAwB,CAAC;AACvC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,sCAAsC,CAAC;AACrD,cAAc,0BAA0B,CAAC;AACzC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,mCAAmC,CAAC;AAClD,cAAc,yCAAyC,CAAC;AACxD,cAAc,wBAAwB,CAAC;AACvC,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,iBAAiB,CAAC;AAChC,cAAc,sBAAsB,CAAC;AACrC,cAAc,oBAAoB,CAAC;AACnC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,6BAA6B,CAAC;AAC5C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,6BAA6B,CAAC;AAC5C,cAAc,yBAAyB,CAAC;AACxC,cAAc,qBAAqB,CAAC;AACpC,cAAc,sCAAsC,CAAC;AACrD,cAAc,qCAAqC,CAAC;AACpD,cAAc,uCAAuC,CAAC;AACtD,cAAc,sCAAsC,CAAC;AACrD,cAAc,yBAAyB,CAAC;AACxC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,0BAA0B,CAAC;AACzC,cAAc,iCAAiC,CAAC;AAChD,cAAc,6BAA6B,CAAC;AAC5C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,0BAA0B,CAAC;AACzC,cAAc,wCAAwC,CAAC;AACvD,cAAc,iBAAiB,CAAC;AAChC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,sBAAsB,CAAC;AACrC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,6BAA6B,CAAC;AAC5C,cAAc,8BAA8B,CAAC;AAC7C,cAAc,sBAAsB,CAAC;AACrC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,yBAAyB,CAAC;AACxC,cAAc,mBAAmB,CAAC;AAClC,cAAc,wBAAwB,CAAC;AACvC,cAAc,wBAAwB,CAAC;AACvC,cAAc,kBAAkB,CAAC;AACjC,cAAc,yBAAyB,CAAC;AACxC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC"}

package/dist/src/index.js

@@ -43,6 +43,7 @@ export * from './web/analyze-api.js';
 export * from './web/mcp-http.js';
 export * from './mcp-resources/index.js';
 export * from './analysis/shape-extractor.js';
+export * from './analysis/git-ref.js';
 export * from './mcp-tools/tool-map.js';
 export * from './mcp-tools/shape-check.js';
 export * from './mcp-tools/neighbors.js';

package/dist/src/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,yBAAyB,CAAC;AACxC,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AACpC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,mBAAmB,CAAC;AAClC,cAAc,qBAAqB,CAAC;AACpC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,kBAAkB,CAAC;AACjC,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,qBAAqB,CAAC;AACpC,cAAc,iBAAiB,CAAC;AAChC,cAAc,sBAAsB,CAAC;AACrC,cAAc,oBAAoB,CAAC;AACnC,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,iBAAiB,CAAC;AAChC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,wBAAwB,CAAC;AACvC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,2BAA2B,CAAC;AAC1C,cAAc,2BAA2B,CAAC;AAC1C,6GAA6G;AAC7G,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,iBAAiB,CAAC;AAChC,cAAc,cAAc,CAAC;AAC7B,cAAc,qBAAqB,CAAC;AACpC,cAAc,mBAAmB,CAAC;AAClC,cAAc,sBAAsB,CAAC;AACrC,cAAc,mBAAmB,CAAC;AAClC,cAAc,0BAA0B,CAAC;AACzC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,uBAAuB,CAAC;AACtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,4FAA4F;AAC5F,cAAc,wBAAwB,CAAC;AACvC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,sCAAsC,CAAC;AACrD,cAAc,0BAA0B,CAAC;AACzC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,mCAAmC,CAAC;AAClD,cAAc,yCAAyC,CAAC;AACxD,cAAc,wBAAwB,CAAC;AACvC,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,iBAAiB,CAAC;AAChC,cAAc,sBAAsB,CAAC;AACrC,cAAc,oBAAoB,CAAC;AACnC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,6BAA6B,CAAC;AAC5C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,6BAA6B,CAAC;AAC5C,cAAc,yBAAyB,CAAC;AACxC,cAAc,qBAAqB,CAAC;AACpC,cAAc,sCAAsC,CAAC;AACrD,cAAc,qCAAqC,CAAC;AACpD,cAAc,uCAAuC,CAAC;AACtD,cAAc,sCAAsC,CAAC;AACrD,cAAc,yBAAyB,CAAC;AACxC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,0BAA0B,CAAC;AACzC,cAAc,iCAAiC,CAAC;AAChD,cAAc,6BAA6B,CAAC;AAC5C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,0BAA0B,CAAC;AACzC,cAAc,wCAAwC,CAAC;AACvD,cAAc,iBAAiB,CAAC;AAChC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,sBAAsB,CAAC;AACrC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,6BAA6B,CAAC;AAC5C,cAAc,8BAA8B,CAAC;AAC7C,cAAc,sBAAsB,CAAC;AACrC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,yBAAyB,CAAC;AACxC,cAAc,mBAAmB,CAAC;AAClC,cAAc,wBAAwB,CAAC;AACvC,cAAc,wBAAwB,CAAC;AACvC,cAAc,kBAAkB,CAAC;AACjC,cAAc,yBAAyB,CAAC;AACxC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC"}

package/dist/src/lsp/server.d.ts

@@ -1,4 +1,4 @@
-import type { MonographDb } from '../storage/db.js';
+import { type MonographDb } from '../storage/db.js';
 export interface LspDiagnostic {
     uri: string;
     range: {

package/dist/src/lsp/server.d.ts.map

@@ -1 +1 @@
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