faf-mcp 4.1.0 → 4.1.2

package/CHANGELOG.md

@@ -1,5 +1,5 @@
 <!-- faf: faf-mcp | TypeScript | mcp | The Interop MCP for Context — the Cursor / IDE Edition. Persistent context for Cursor, VS Code, and every MCP-compatible IDE. IANA-registered application/vnd.faf+yaml. Start with "Use FAF". -->
-<!-- faf: doc=changelog | latest=v4.1.0 | canonical=project.faf | family=FAF -->
+<!-- faf: doc=changelog | latest=v4.1.2 | canonical=project.faf | family=FAF -->
 
 # Changelog
 
@@ -8,6 +8,23 @@ All notable changes to faf-mcp will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [4.1.2] - 2026-11-05 — The Instructions Edition
+
+**faf_write can no longer overwrite the birth certificate or your context files, and faf_dna never issues a second one.**
+
+### Fixed
+- **`faf_write` refuses `.faf-dna`** in every spelling and route (case, `..`, absolute paths, symlinks, symlinked folders, `.faf-dna/x`), with or without `overwrite: true` ([#110](https://github.com/Wolfe-Jam/faf-mcp/pull/110)).
+- **Existing `project.faf`, `*.faf`, `CLAUDE.md` and `AGENTS.md` need `overwrite: true`.** New files write as before. Writes stay inside the project folder, never in `.git/`, checked on the resolved real path, and land atomically with file permissions kept.
+- **`faf_dna` issues one birth certificate, once.** Concurrent calls create exactly one. If `.faf-dna` is missing but git history shows it existed (any branch, the reflog, a stash, a linked worktree, a `--shared` clone's source), it refuses and prints the restore steps. If history can't be checked, it refuses rather than guess ([#110](https://github.com/Wolfe-Jam/faf-mcp/pull/110), [#111](https://github.com/Wolfe-Jam/faf-mcp/pull/111)).
+- **Restore steps** list the latest version first: `git log --all --reflog --diff-filter=AM --oneline -- .faf-dna`, then `git checkout <sha> -- .faf-dna`.
+
+## [4.1.1] - 2026-10-28 — The Instructions Edition
+
+**One rule for project questions: read project.faf first.**
+
+### Changed
+- **Server instructions: a rule for project questions.** Line 2 now reads "For questions about the project (stack, goal, commands), read project.faf first and answer from it. faf_score shows what is missing; faf_doctor says why." It replaces "Start with faf_doctor or faf_score…", which models read as a hint: in a 3-run pilot on a repo where project.faf and package.json disagree, Claude Code and Grok Build read package.json first 3 of 3 with the old line, and project.faf first 3 of 3 (Claude) and 2 of 3 (Grok) with the new one. 712 characters.
+
 ## [4.1.0] - 2026-10-27 — The Instructions Edition
 
 **faf-mcp now tells the model how its tools fit together: server instructions in initialize (642 characters), plus faf-cli 8.5.0, which knows a skills repo when it sees one.** 413 tests pass, 0 fail.

package/CLAUDE.md

@@ -25,12 +25,12 @@ The Interop MCP for Context — the Cursor / IDE Edition. Persistent context for
 - **What:** The Cursor / IDE Edition — persistent context for Cursor, VS Code, and every MCP-compatible IDE — 29 MCP tools (15 essential shown by default), interop with AGENTS.md, .cursorrules, GEMINI.md
 - **Why:** Eliminate the 20-minute AI context tax — give AI instant project understanding in 30 seconds
 - **Where:** npm · MCP Registry · any MCP-compatible IDE — people get it how they wish
-- **When:** Production/Stable — v4.1.0 The Instructions Edition, WJTTC certified
+- **When:** Production/Stable — v4.1.2 The Instructions Edition, WJTTC certified
 - **How:** npx faf-mcp or npm install -g faf-mcp, then add to your MCP config
 
 ---
 
-*STATUS: SYNC ACTIVE — 2026-10-27T21:01:01.358Z*
+*STATUS: SYNC ACTIVE — 2026-11-05T14:10:38.504Z*
 <!-- faf:end -->
 
 ## Working here

package/README.md

@@ -19,7 +19,7 @@
 
 **.FAF Context** is the MCP server for the IDE side of FAF. One `project.faf` in your repo, and every AI tool's context file is authored from it — AGENTS.md, .cursorrules, GEMINI.md, CLAUDE.md — and scored, so you know exactly where to focus. It runs locally over stdio on the same faf-cli the terminal uses. The FAF ecosystem it belongs to has comfortably passed 100k downloads across npm and PyPI ([live count](https://faf.one/downloads)).
 
-⭐ Bookmarks it for you, helps other devs find it too.
+⭐ [Star it on GitHub](https://github.com/Wolfe-Jam/faf-mcp): bookmarks it for you, helps other devs find it too.
 
 [![CI](https://github.com/Wolfe-Jam/faf-mcp/actions/workflows/ci.yml/badge.svg)](https://github.com/Wolfe-Jam/faf-mcp/actions/workflows/ci.yml)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
@@ -28,7 +28,17 @@
 
 ---
 
-## What's New in 4.1.0 — The Instructions Edition
+## What's New in 4.1.2 — The Instructions Edition
+
+**faf_write can no longer overwrite the birth certificate or your context files, and faf_dna never issues a second one.** `.faf-dna` is refused in every spelling and route, existing context files need `overwrite: true`, and `faf_dna` refuses rather than reissue when git shows a certificate existed.
+
+## 4.1.1
+
+**One rule for project questions: read project.faf first.**
+
+- **Server instructions, line 2.** "For questions about the project (stack, goal, commands), read project.faf first and answer from it. faf_score shows what is missing; faf_doctor says why." It replaces "start with `faf_doctor` or `faf_score`", which agents read as a hint. In a 3-run pilot on a repo where project.faf and package.json disagree, Claude Code read project.faf first 3 of 3 and Grok Build 2 of 3 with the new line, against 0 of 3 for both with the old one. 712 characters.
+
+## 4.1.0 — The Instructions Edition
 
 **faf-mcp now tells the model how its tools fit together: server instructions in initialize (642 characters), plus faf-cli 8.5.0, which knows a skills repo when it sees one.**
 
@@ -225,7 +235,7 @@ The 15 Core tools, shown by default:
 | `faf_gemini` | Import GEMINI.md into `project.faf`, or write it from `project.faf` |
 | `faf_git` | Author a `project.faf` from a public GitHub repo URL |
 
-**+14 more with `FAF_TOOLS=all`:** `faf_status` · `faf_what` · `faf_guide` · `faf_debug` · `faf_clear` · `faf_list` · `faf_read` (read a file within the allowed roots: cwd, the OS temp dir, or `FAF_ALLOWED_ROOTS`) · `faf_write` (write a file within the same roots) · `faf_readme` · `faf_human_add` · `faf_quick` · `faf_formats` · `faf_dna` · `faf_conductor`
+**+14 more with `FAF_TOOLS=all`:** `faf_status` · `faf_what` · `faf_guide` · `faf_debug` · `faf_clear` · `faf_list` · `faf_read` (read a file within the allowed roots: cwd, the OS temp dir, or `FAF_ALLOWED_ROOTS`) · `faf_write` (write a file within cwd or `FAF_ALLOWED_ROOTS`; never `.faf-dna` or `.git/`; an existing `*.faf`, `CLAUDE.md` or `AGENTS.md` needs `overwrite: true`) · `faf_readme` · `faf_human_add` · `faf_quick` · `faf_formats` · `faf_dna` · `faf_conductor`
 
 **Built on faf-cli.** Every tool composes the bundled [faf-cli](https://www.npmjs.com/package/faf-cli) in-process — the same scorer, the same renderers, the same block injector the CLI uses. Nothing shells out to a `faf` on your PATH.
 

package/dist/src/handlers/fileHandler.d.ts

@@ -26,6 +26,12 @@ export declare const fafWriteTool: Tool;
  * Handle faf_read tool execution
  */
 export declare function handleFafRead(args: any): Promise<CallToolResult>;
+/**
+ * Context files faf_write will not replace unless the caller passes
+ * `overwrite: true`: any `*.faf` (project.faf, .faf), CLAUDE.md and AGENTS.md.
+ * Case-insensitive, so a case-insensitive filesystem cannot slip past.
+ */
+export declare function isProtectedContextFile(p: string): boolean;
 /**
  * Handle faf_write tool execution
  */

package/dist/src/handlers/fileHandler.js

@@ -37,9 +37,12 @@ var __importStar = (this && this.__importStar) || (function () {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fileHandlers = exports.fafWriteTool = exports.fafReadTool = exports.PathValidator = void 0;
 exports.handleFafRead = handleFafRead;
+exports.isProtectedContextFile = isProtectedContextFile;
 exports.handleFafWrite = handleFafWrite;
 const fs = __importStar(require("fs/promises"));
 const path = __importStar(require("path"));
+const fsSync = __importStar(require("fs"));
+const crypto = __importStar(require("crypto"));
 const safe_path_1 = require("../utils/safe-path");
 /**
  * Security validator for file paths
@@ -103,7 +106,7 @@ exports.fafReadTool = {
  */
 exports.fafWriteTool = {
     name: 'faf_write',
-    description: 'Write content to any file on the local filesystem',
+    description: 'Write a file within the project root (cwd, or FAF_ALLOWED_ROOTS when set). Paths outside it, inside .git/, and .faf-dna (the birth certificate) are always refused. An existing *.faf, CLAUDE.md or AGENTS.md is not replaced unless overwrite is true. Writes via temp file + rename.',
     inputSchema: {
         type: 'object',
         properties: {
@@ -111,6 +114,10 @@ exports.fafWriteTool = {
                 type: 'string',
                 description: 'Absolute or relative file path to write'
             },
+            overwrite: {
+                type: 'boolean',
+                description: 'Set true to replace an existing *.faf, CLAUDE.md or AGENTS.md. Without it, faf_write refuses and leaves the file unchanged. Never applies to .faf-dna.'
+            },
             content: {
                 type: 'string',
                 description: 'Content to write to the file'
@@ -182,18 +189,107 @@ async function handleFafRead(args) {
         };
     }
 }
+/**
+ * Context files faf_write will not replace unless the caller passes
+ * `overwrite: true`: any `*.faf` (project.faf, .faf), CLAUDE.md and AGENTS.md.
+ * Case-insensitive, so a case-insensitive filesystem cannot slip past.
+ */
+function isProtectedContextFile(p) {
+    const base = path.basename(p).toLowerCase();
+    return base.endsWith('.faf') || base === 'claude.md' || base === 'agents.md';
+}
+/**
+ * Write `content` to `target` via a temp file in the same directory, then
+ * rename (replace) or link (no-clobber) it into place. A reader never sees a
+ * half-written file. With `noClobber`, an existing target is never replaced,
+ * even if it appears between the caller's check and this write: link() fails
+ * with EEXIST atomically.
+ */
+async function atomicWrite(target, content, noClobber) {
+    const dir = path.dirname(target);
+    const tmp = path.join(dir, `.${path.basename(target)}.faf-tmp-${process.pid}-${crypto.randomBytes(4).toString('hex')}`);
+    await fs.writeFile(tmp, content, { encoding: 'utf8', flag: 'wx' });
+    try {
+        if (!noClobber) {
+            // Keep the replaced file's permission bits (0755 stays 0755). The temp
+            // file was created with the default mode, so copy the old one across.
+            await keepMode(target, tmp);
+            await fs.rename(tmp, target);
+            return;
+        }
+        try {
+            await fs.link(tmp, target);
+        }
+        catch (err) {
+            if (errCode(err) === 'EEXIST')
+                throw err;
+            // Filesystem without hard links: exclusive copy is still no-clobber.
+            await fs.copyFile(tmp, target, fsSync.constants.COPYFILE_EXCL);
+        }
+    }
+    finally {
+        await fs.rm(tmp, { force: true });
+    }
+}
+/** Copy `from`'s permission bits onto `to`. No-op when `from` does not exist. */
+async function keepMode(from, to) {
+    let mode;
+    try {
+        mode = (await fs.stat(from)).mode & 0o7777;
+    }
+    catch (err) {
+        if (errCode(err) === 'ENOENT')
+            return;
+        throw err;
+    }
+    await fs.chmod(to, mode);
+}
+function errCode(err) {
+    return typeof err === 'object' && err !== null && 'code' in err ? String(err.code) : undefined;
+}
+function existsNoFollow(p) {
+    try {
+        fsSync.lstatSync(p);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+function refuseExisting(filePath) {
+    return {
+        content: [{
+                type: 'text',
+                text: `❌ Refused: ${filePath} already exists and is a protected context file ` +
+                    `(*.faf, CLAUDE.md, AGENTS.md). faf_write did not change it.\n` +
+                    `To replace it, call faf_write again with overwrite: true. ` +
+                    `To update project.faf or CLAUDE.md without losing hand-written content, ` +
+                    `use the dedicated faf tools instead.`
+            }],
+        isError: true
+    };
+}
 /**
  * Handle faf_write tool execution
  */
 async function handleFafWrite(args) {
     const startTime = Date.now();
     try {
-        const { path: rawPath, content } = args;
-        // Confine to the project root(s) before any write — closes arbitrary file
-        // write outside the project (e.g. overwriting ~/.bashrc).
+        const input = (args ?? {});
+        const rawPath = input.path;
+        const content = input.content;
+        const overwrite = input.overwrite === true;
+        if (typeof content !== 'string') {
+            return {
+                content: [{ type: 'text', text: '❌ content must be a string' }],
+                isError: true
+            };
+        }
+        // Confine to the project root before any write: cwd only (or an explicit
+        // FAF_ALLOWED_ROOTS), never .git/, never .faf-dna, real path resolved.
         let filePath;
         try {
-            filePath = (0, safe_path_1.confineFileOp)(rawPath);
+            filePath = (0, safe_path_1.confineWriteOp)(rawPath);
         }
         catch (err) {
             if (err instanceof safe_path_1.PathConfinementError) {
@@ -215,24 +311,36 @@ async function handleFafWrite(args) {
                 isError: true
             };
         }
+        const protectedFile = isProtectedContextFile(filePath) || isProtectedContextFile(String(rawPath));
+        const noClobber = protectedFile && !overwrite;
+        if (noClobber && existsNoFollow(filePath)) {
+            return refuseExisting(filePath);
+        }
         // Create directory if needed
         const dir = path.dirname(filePath);
         await fs.mkdir(dir, { recursive: true });
         // Write file with timeout
-        await Promise.race([
-            fs.writeFile(filePath, content, 'utf8'),
-            new Promise((_, reject) => setTimeout(() => reject(new Error('Write timeout (30s)')), 30000))
-        ]);
+        try {
+            await Promise.race([
+                atomicWrite(filePath, content, noClobber),
+                new Promise((_, reject) => setTimeout(() => reject(new Error('Write timeout (30s)')), 30000).unref?.())
+            ]);
+        }
+        catch (err) {
+            if (noClobber && errCode(err) === 'EEXIST')
+                return refuseExisting(filePath);
+            throw err;
+        }
         const duration = Date.now() - startTime;
         return {
             content: [{
                     type: 'text',
-                    text: `✅ Successfully wrote ${contentSize} bytes to ${path.resolve(filePath)}`
+                    text: `✅ Successfully wrote ${contentSize} bytes to ${filePath}`
                 }],
             metadata: {
                 duration_ms: duration,
                 bytes_written: contentSize,
-                file_path: path.resolve(filePath),
+                file_path: filePath,
                 message: `✅ Write completed in ${duration}ms`
             }
         };

package/dist/src/handlers/fileHandler.js.map

@@ -1 +1 @@
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package/dist/src/handlers/tools.js

@@ -36,6 +36,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.FafToolHandler = void 0;
 const fileHandler_1 = require("./fileHandler");
 const fs = __importStar(require("fs"));
+const git_history_1 = require("../utils/git-history");
 const os = __importStar(require("os"));
 const pathModule = __importStar(require("path"));
 const faf_file_finder_js_1 = require("../utils/faf-file-finder.js");
@@ -295,7 +296,7 @@ class FafToolHandler {
             },
             {
                 name: 'faf_write',
-                description: 'Write a file within the allowed roots (cwd, the OS temp dir, or FAF_ALLOWED_ROOTS). Paths outside them are refused.',
+                description: 'Write a file within the project root (cwd, or FAF_ALLOWED_ROOTS when set). Paths outside it, inside .git/, and .faf-dna (the birth certificate) are always refused. An existing *.faf, CLAUDE.md or AGENTS.md is not replaced unless overwrite is true. Writes via temp file + rename.',
                 annotations: {
                     title: 'Write Project File',
                     readOnlyHint: false,
@@ -309,6 +310,10 @@ class FafToolHandler {
                             type: 'string',
                             description: 'Absolute or relative file path to write'
                         },
+                        overwrite: {
+                            type: 'boolean',
+                            description: 'Set true to replace an existing *.faf, CLAUDE.md or AGENTS.md. Without it, faf_write refuses and leaves the file unchanged. Never applies to .faf-dna.'
+                        },
                         content: {
                             type: 'string',
                             description: 'Content to write to the file'
@@ -2053,6 +2058,34 @@ Call these MCP tools:
                             }]
                     };
                 }
+                // A .faf-dna that was ever committed is a birth that already happened.
+                // Reissuing would replace the certificate; restore it from git instead.
+                const history = (0, git_history_1.gitEverTracked)(dnaPath);
+                if (history.status === 'found') {
+                    const committed = history.where;
+                    return {
+                        content: [{
+                                type: 'text',
+                                text: `🧬 FAF DNA Journey\n\n❌ .faf-dna is missing, but git shows it existed (${committed}).\nThe birth certificate is issued once and is not reissued.\n\n💡 Restore it from git instead:\n   git log --all --reflog --diff-filter=AM --oneline -- .faf-dna   (the first line is the latest version, reflog included)\n   git checkout <sha> -- .faf-dna                 (restore that version)`
+                            }],
+                        isError: true
+                    };
+                }
+                // Fail closed: if git history could not be read in full, a deleted
+                // certificate cannot be ruled out, so none is issued.
+                if (history.status === 'unknown') {
+                    return {
+                        content: [{
+                                type: 'text',
+                                text: `🧬 FAF DNA Journey\n\n❌ .faf-dna is missing and git history could not be checked (${history.reason}).\nThe birth certificate is issued once and is not reissued, so faf_dna did not create one.\n\n💡 If .faf-dna existed before, restore it from git:\n   git log --all --reflog --diff-filter=AM --oneline -- .faf-dna   (the first line is the latest version, reflog included)\n   git checkout <sha> -- .faf-dna                 (restore that version)\n💡 If this really is a brand-new project, create the first one with faf-cli:\n   faf init`
+                            }],
+                        isError: true
+                    };
+                }
+                // Outside git there is no history to check: say so in the reply.
+                const noHistoryNote = history.status === 'not-a-repo'
+                    ? `\n\n⚠️ Not a git repository: no history could be checked, so a lost .faf-dna cannot be told apart from a new project. If this project had a .faf-dna before, replace this one with the restored original.`
+                    : '';
                 // .faf exists but no DNA - create initial DNA. Real scorer — same
                 // one faf_score reads — never a local pseudo-score (v3.0 fix).
                 const { readFafRaw, scoreFafYaml } = await faf_cli_bridge_js_1.fafCli;
@@ -2075,11 +2108,28 @@ Call these MCP tools:
                     ],
                     format: 'faf-dna-v1'
                 };
-                fs.writeFileSync(dnaPath, JSON.stringify(dna, null, 2));
+                // Exclusive create (O_EXCL): the birth certificate is written once.
+                // If another call created it in the meantime, that one stands and is
+                // the one reported — never a second certificate.
+                try {
+                    fs.writeFileSync(dnaPath, JSON.stringify(dna, null, 2), { flag: 'wx' });
+                }
+                catch (err) {
+                    if (err?.code !== 'EEXIST')
+                        throw err;
+                    const existing = JSON.parse(fs.readFileSync(dnaPath, 'utf-8'));
+                    const bc = existing.birthCertificate ?? {};
+                    return {
+                        content: [{
+                                type: 'text',
+                                text: `🧬 FAF DNA Journey\n\n🎫 Birth Certificate already exists — not reissued.\n\n📊 Birth DNA: ${bc.birthDNA ?? 0}%\n📅 Born: ${String(bc.born ?? '').split('T')[0]}\n🎫 Certificate: ${bc.certificate ?? 'unknown'}`
+                            }]
+                    };
+                }
                 return {
                     content: [{
                             type: 'text',
-                            text: `🧬 FAF DNA Journey\n\n🐣 Birth Certificate Created!\n\n📊 Birth DNA: ${currentScore}%\n📅 Born: ${new Date().toISOString().split('T')[0]}\n🎫 Certificate: ${dna.birthCertificate.certificate}\n\n💡 Your journey begins here! Run faf_auto or faf_go to grow.`
+                            text: `🧬 FAF DNA Journey\n\n🐣 Birth Certificate Created!\n\n📊 Birth DNA: ${currentScore}%\n📅 Born: ${new Date().toISOString().split('T')[0]}\n🎫 Certificate: ${dna.birthCertificate.certificate}\n\n💡 Your journey begins here! Run faf_auto or faf_go to grow.${noHistoryNote}`
                         }]
                 };
             }
@@ -2102,7 +2152,12 @@ Call these MCP tools:
                     const now = new Date().toISOString();
                     dna.current = { ...(dna.current ?? {}), score: live, lastSync: now };
                     milestones.push({ type: 'sync', score: live, date: now, version: dna.current.version ?? 'v1.0.0' });
-                    fs.writeFileSync(dnaPath, JSON.stringify(dna, null, 2));
+                    // birthCertificate is carried over unchanged; temp + rename so a
+                    // crash mid-write cannot truncate the certificate.
+                    const tmpDna = `${dnaPath}.tmp-${process.pid}-${Date.now()}`;
+                    fs.writeFileSync(tmpDna, JSON.stringify(dna, null, 2), { flag: 'wx' });
+                    fs.chmodSync(tmpDna, fs.statSync(dnaPath).mode & 0o7777); // keep the certificate's mode
+                    fs.renameSync(tmpDna, dnaPath);
                     currentScore = live;
                 }
             }