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Update versions & CHANGELOG for v2.25.1-next.2 (#200)
Prep for the v2.25.1-next.2 release as a hotfix for the v2.25.1-next.1 release.
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‎CHANGELOG.md‎

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@@ -20,7 +20,7 @@ _Changes on `main` since the latest tagged release that have not yet been includ
2020

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- **Persistent MRVA workflow state and caching** — Introduced a new `SqliteStore` backend plus opt-in annotation, audit, and query result cache tools to support the next phase of MCP-assisted CodeQL development and `seclab-taskflow-agent` integration. ([#169](https://github.com/advanced-security/codeql-development-mcp-server/pull/169))
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- **Rust language support** — Added first-class Rust support with `PrintAST`, `PrintCFG`, `CallGraphFrom`, `CallGraphTo`, and `CallGraphFromTo` queries, bringing the total supported languages to 10. ([#195](https://github.com/advanced-security/codeql-development-mcp-server/pull/195))
23-
- **VS Code workspace change reliability** — Fixed MCP server restart behavior when workspace folders change so the extension now restarts the server with a fresh environment instead of leaving it partially stopped. ([#196](https://github.com/advanced-security/codeql-development-mcp-server/pull/196))
23+
- **Bug fixes and design improvements from v2.25.1-next.1 evaluation** — Fixed 5 bugs across `bqrs_interpret`, `bqrs_info`, `annotation_search`, `audit_add_notes`, and `query_results_cache_compare`; added `database_analyze` auto-caching and per-database mutex serialization; auto-enabled annotation tools in VS Code extension. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
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### Added
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@@ -53,15 +53,22 @@ _Changes on `main` since the latest tagged release that have not yet been includ
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#### MCP Server Tools
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56-
| Tool | Change |
57-
| -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
58-
| `codeql_query_run` | Query results are now auto-cached after SARIF interpretation, enabling later lookup and comparison workflows. ([#169](https://github.com/advanced-security/codeql-development-mcp-server/pull/169)) |
59-
| query metadata and database resolution | Added in-memory caching with mtime-based invalidation and deduplicated resolution logic for better performance. ([#169](https://github.com/advanced-security/codeql-development-mcp-server/pull/169)) |
56+
| Tool | Change |
57+
| -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
58+
| `codeql_query_run` | Query results are now auto-cached after SARIF interpretation, enabling later lookup and comparison workflows. ([#169](https://github.com/advanced-security/codeql-development-mcp-server/pull/169)) |
59+
| query metadata and database resolution | Added in-memory caching with mtime-based invalidation and deduplicated resolution logic for better performance. ([#169](https://github.com/advanced-security/codeql-development-mcp-server/pull/169)) |
60+
| `codeql_bqrs_interpret` | Added optional `database` parameter mapped to `--source-archive` for SARIF source context; validates that `src.zip` or `src` exists. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199)) |
61+
| `codeql_bqrs_info` | **Breaking**: renamed `files` (array) parameter to `file` (string) to match the CLI which accepts exactly one file. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199)) |
62+
| `codeql_database_analyze` | Results are now auto-cached after SARIF output for `query_results_cache_compare` and `query_results_cache_retrieve`; concurrent calls to the same database are serialized via a per-database mutex. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199)) |
63+
| `audit_add_notes` | Added `findingId` as preferred lookup; `owner`/`repo`/`sourceLocation`/`line` are now optional fallback fields. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199)) |
64+
| `annotation_search` | Category field is now matched with case-insensitive `COLLATE NOCASE` alongside the existing FTS index. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199)) |
65+
| `query_results_cache_compare` | SARIF content fallback for result count is now gated on SARIF output format, avoiding unnecessary JSON parsing of non-SARIF cache entries. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199)) |
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#### VS Code Extension
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- `McpProvider.requestRestart()` now invalidates the environment cache and bumps a `+rN` revision suffix so VS Code reliably restarts the MCP server after configuration changes. ([#196](https://github.com/advanced-security/codeql-development-mcp-server/pull/196))
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- Cached the extension version in the provider constructor to avoid repeated synchronous reads of `package.json`. ([#196](https://github.com/advanced-security/codeql-development-mcp-server/pull/196))
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- New `codeql-mcp.enableAnnotationTools` setting (default: `true`) auto-sets `ENABLE_ANNOTATION_TOOLS` and `MONITORING_STORAGE_LOCATION` environment variables; `additionalEnv` overrides for advanced users. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
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#### Infrastructure & CI/CD
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@@ -70,6 +77,12 @@ _Changes on `main` since the latest tagged release that have not yet been includ
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### Fixed
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- **Workspace folder changes could leave the MCP server stopped but not restarted** — The VS Code extension now rebuilds the environment and forces a proper restart when workspace folders change. ([#196](https://github.com/advanced-security/codeql-development-mcp-server/pull/196))
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- **`codeql_bqrs_interpret` unusable through MCP interface** — Added `database` parameter mapped to `--source-archive` with `src.zip`/`src` fallback and clear error when neither exists. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
81+
- **`query_results_cache_compare` reported `totalResultCount: 0`** — Result count is now computed from SARIF `runs[0].results.length` at cache time; compare tool falls back to parsing cached SARIF content only for SARIF-format entries. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
82+
- **`annotation_search` ignored `category` field** — Extended FTS search condition to also match category with case-insensitive `COLLATE NOCASE`. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
83+
- **`audit_add_notes` ignored `findingId`** — Added `findingId` as preferred direct-lookup alternative to the composite key fields. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
84+
- **`codeql_bqrs_info` `files` array caused CLI error** — Changed parameter from `files` (array) to `file` (string) to match the CLI expectation. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
85+
- **Per-database mutex lock key not normalized** — Database lock key now uses `realpath` to prevent bypassing serialization with relative paths, symlinks, or different casing. ([#199](https://github.com/advanced-security/codeql-development-mcp-server/pull/199))
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### Dependencies
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‎client/package.json‎

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{
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"name": "codeql-development-mcp-server_client",
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"version": "2.25.1-next.1",
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"version": "2.25.1-next.2",
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"description": "MCP client for integration testing of the CodeQL development MCP server",
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"main": "src/ql-mcp-client.js",
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"type": "module",

‎extensions/vscode/package.json‎

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"name": "vscode-codeql-development-mcp-server",
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"displayName": "CodeQL Development MCP Server",
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"description": "LLM-assisted development of CodeQL queries, libraries, and tests via #ql-mcp prompts, resources, and tools.",
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"version": "2.25.1-next.1",
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"version": "2.25.1-next.2",
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"publisher": "advanced-security",
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"license": "SEE LICENSE IN LICENSE",
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"icon": "media/codeql-icon.png",

‎package-lock.json‎

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‎package.json‎

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{
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"name": "codeql-development-mcp-server_repo",
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"version": "2.25.1-next.1",
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"version": "2.25.1-next.2",
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"description": "An MCP server supporting LLM requests for CodeQL development tools and resources.",
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"private": true,
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"type": "module",

‎server/dist/codeql-development-mcp-server.js‎

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@@ -182798,7 +182798,7 @@ var StreamableHTTPServerTransport = class {
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var import_express = __toESM(require_express2(), 1);
182799182799
var import_cors = __toESM(require_lib4(), 1);
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var import_dotenv = __toESM(require_main(), 1);
182801-
import { realpathSync as realpathSync2 } from "fs";
182801+
import { realpathSync as realpathSync3 } from "fs";
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import { resolve as resolve14 } from "path";
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import { pathToFileURL as pathToFileURL5 } from "url";
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@@ -184635,7 +184635,7 @@ function cacheDatabaseAnalyzeResults(params, logger2) {
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184636184636
// src/lib/cli-tool-registry.ts
184637184637
init_package_paths();
184638-
import { writeFileSync as writeFileSync4, rmSync, existsSync as existsSync6, mkdirSync as mkdirSync8 } from "fs";
184638+
import { writeFileSync as writeFileSync4, rmSync, existsSync as existsSync6, mkdirSync as mkdirSync8, realpathSync } from "fs";
184639184639
import { delimiter as delimiter5, dirname as dirname5, isAbsolute as isAbsolute4, join as join10, resolve as resolve4 } from "path";
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// ../node_modules/js-yaml/dist/js-yaml.mjs
@@ -187490,7 +187490,16 @@ function registerCLITool(server, definition) {
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const dbPath = resolveDatabasePath(options.database);
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const srcZipPath = join10(dbPath, "src.zip");
187492187492
const srcDirPath = join10(dbPath, "src");
187493-
options["source-archive"] = existsSync6(srcZipPath) ? srcZipPath : srcDirPath;
187493+
if (existsSync6(srcZipPath)) {
187494+
options["source-archive"] = srcZipPath;
187495+
} else if (existsSync6(srcDirPath)) {
187496+
options["source-archive"] = srcDirPath;
187497+
} else {
187498+
delete options.database;
187499+
throw new Error(
187500+
`CodeQL database at "${dbPath}" does not contain a source archive (expected "src.zip" file or "src" directory).`
187501+
);
187502+
}
187494187503
delete options.database;
187495187504
}
187496187505
break;
@@ -187590,7 +187599,12 @@ function registerCLITool(server, definition) {
187590187599
}
187591187600
let dbLock;
187592187601
if (name === "codeql_database_analyze" && positionalArgs.length > 0) {
187593-
dbLock = acquireDatabaseLock(positionalArgs[0]);
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let lockKey = resolve4(positionalArgs[0]);
187603+
try {
187604+
lockKey = realpathSync(lockKey);
187605+
} catch {
187606+
}
187607+
dbLock = acquireDatabaseLock(lockKey);
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await dbLock.ready;
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}
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try {
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};
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// src/tools/codeql/search-ql-code.ts
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import { closeSync as closeSync2, createReadStream as createReadStream3, fstatSync as fstatSync2, lstatSync, openSync as openSync2, readdirSync as readdirSync8, readFileSync as readFileSync12, realpathSync } from "fs";
190394+
import { closeSync as closeSync2, createReadStream as createReadStream3, fstatSync as fstatSync2, lstatSync, openSync as openSync2, readdirSync as readdirSync8, readFileSync as readFileSync12, realpathSync as realpathSync2 } from "fs";
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import { basename as basename8, extname as extname2, join as join19, resolve as resolve9 } from "path";
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import { createInterface as createInterface3 } from "readline";
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init_logger();
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if (SKIP_DIRS2.has(basename8(p))) return;
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let realPath;
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try {
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realPath = realpathSync(p);
190424+
realPath = realpathSync2(p);
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} catch {
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return;
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}
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for (const e of dbEntries) {
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if (e.resultCount != null) {
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totalResultCount += e.resultCount;
194007-
} else {
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} else if (e.outputFormat.includes("sarif")) {
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try {
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init_logger();
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import_dotenv.default.config({ path: resolve14(packageRootDir, ".env"), quiet: true });
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var PACKAGE_NAME = "codeql-development-mcp-server";
194049-
var VERSION = "2.25.1-next.1";
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var VERSION = "2.25.1-next.2";
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async function startServer(mode = "stdio") {
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logger.info(`Starting CodeQL Development MCP McpServer v${VERSION} in ${mode} mode`);
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const codeqlBinary = resolveCodeQLBinary();
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process.exit(1);
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}
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}
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var scriptPath = process.argv[1] ? realpathSync2(resolve14(process.argv[1])) : void 0;
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var scriptPath = process.argv[1] ? realpathSync3(resolve14(process.argv[1])) : void 0;
194147194161
if (scriptPath && import.meta.url === pathToFileURL5(scriptPath).href) {
194148194162
main();
194149194163
}

‎server/dist/codeql-development-mcp-server.js.map‎

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‎server/package.json‎

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{
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"name": "codeql-development-mcp-server",
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"version": "2.25.1-next.1",
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"version": "2.25.1-next.2",
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"description": "An MCP server supporting LLM requests for CodeQL development tools and resources.",
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"main": "dist/codeql-development-mcp-server.js",
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"type": "module",

‎server/ql/actions/tools/src/codeql-pack.yml‎

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name: advanced-security/ql-mcp-actions-tools-src
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version: 2.25.1-next.1
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version: 2.25.1-next.2
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description: 'Queries for codeql-development-mcp-server tools for actions language'
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library: false
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dependencies:

‎server/ql/actions/tools/test/codeql-pack.yml‎

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name: advanced-security/ql-mcp-actions-tools-test
2-
version: 2.25.1-next.1
2+
version: 2.25.1-next.2
33
dependencies:
44
advanced-security/ql-mcp-actions-tools-src: ${workspace}
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extractor: actions

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