@commentray/mcp-server 0.4.1

package/dist/index.d.ts

@@ -0,0 +1,5 @@
+export { createMcpServer } from "./mcp-server.js";
+export { installMcpConfigs, type InstallMcpConfigsOptions, type HarnessConfig, } from "./mcp-install.js";
+export { ALL_TOOLS, type McpToolDef } from "./mcp-tools.js";
+export { repoRootFrom } from "./repo-root.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -0,0 +1,5 @@
+export { createMcpServer } from "./mcp-server.js";
+export { installMcpConfigs, } from "./mcp-install.js";
+export { ALL_TOOLS } from "./mcp-tools.js";
+export { repoRootFrom } from "./repo-root.js";
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/mcp-install.d.ts

@@ -0,0 +1,29 @@
+export interface HarnessConfig {
+    /** Human-readable harness name */
+    name: string;
+    /** Path relative to repo root for the MCP config file */
+    configFileRel: string;
+    /** Whether this harness is always written (true) or only if its directory already exists */
+    alwaysWrite: boolean;
+}
+export interface InstallMcpConfigsOptions {
+    dryRun?: boolean;
+    force?: boolean;
+}
+export interface InstallResult {
+    harness: string;
+    configFile: string;
+    action: "created" | "updated" | "skipped" | "would_create" | "would_update";
+}
+/**
+ * Install (or update) repo-local MCP config files for all supported harnesses.
+ *
+ * Each config file references `commentray mcp serve` as the command — fully
+ * portable, no absolute paths. Safe to commit to a multi-contributor repo.
+ *
+ * @param repoRoot Absolute path to the repo root
+ * @param options dryRun (preview only), force (overwrite existing commentray entry)
+ * @returns Array of results describing what happened for each harness
+ */
+export declare function installMcpConfigs(repoRoot: string, options?: InstallMcpConfigsOptions): Promise<InstallResult[]>;
+//# sourceMappingURL=mcp-install.d.ts.map

package/dist/mcp-install.d.ts.map

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package/dist/mcp-install.js

@@ -0,0 +1,92 @@
+import fs from "node:fs/promises";
+import path from "node:path";
+// ── Harness definitions ───────────────────────────────────────────────────
+const HARNESSES = [
+    { name: "VS Code Copilot", configFileRel: ".vscode/mcp.json", alwaysWrite: true },
+    { name: "Claude Code", configFileRel: ".claude/mcp.json", alwaysWrite: true },
+    { name: "Antigravity", configFileRel: ".antigravity/mcp.json", alwaysWrite: true },
+    { name: "OpenCode", configFileRel: ".opencode/mcp.json", alwaysWrite: true },
+];
+// ── MCP server entry (portable — no absolute paths) ───────────────────────
+function makeMcpEntry() {
+    return {
+        commentray: {
+            type: "stdio",
+            command: "commentray",
+            args: ["mcp", "serve"],
+            cwd: "${workspaceFolder}",
+        },
+    };
+}
+async function readOrEmpty(absPath) {
+    try {
+        const raw = await fs.readFile(absPath, "utf8");
+        return JSON.parse(raw);
+    }
+    catch {
+        return {};
+    }
+}
+// ── Install function ──────────────────────────────────────────────────────
+/**
+ * Install (or update) repo-local MCP config files for all supported harnesses.
+ *
+ * Each config file references `commentray mcp serve` as the command — fully
+ * portable, no absolute paths. Safe to commit to a multi-contributor repo.
+ *
+ * @param repoRoot Absolute path to the repo root
+ * @param options dryRun (preview only), force (overwrite existing commentray entry)
+ * @returns Array of results describing what happened for each harness
+ */
+export async function installMcpConfigs(repoRoot, options = {}) {
+    const results = [];
+    for (const harness of HARNESSES) {
+        const configAbs = path.join(repoRoot, harness.configFileRel);
+        // Check if directory exists for non-always-write harnesses
+        if (!harness.alwaysWrite) {
+            try {
+                await fs.access(path.dirname(configAbs));
+            }
+            catch {
+                continue; // skip — harness not present
+            }
+        }
+        const existing = await readOrEmpty(configAbs);
+        const hasCommentray = existing.servers && "commentray" in existing.servers;
+        if (hasCommentray && !options.force) {
+            results.push({
+                harness: harness.name,
+                configFile: harness.configFileRel,
+                action: "skipped",
+            });
+            continue;
+        }
+        const action = hasCommentray ? "updated" : "created";
+        const dryAction = hasCommentray ? "would_update" : "would_create";
+        if (options.dryRun) {
+            results.push({
+                harness: harness.name,
+                configFile: harness.configFileRel,
+                action: dryAction,
+            });
+            continue;
+        }
+        // Merge the Commentray entry into the existing config
+        const merged = {
+            ...existing,
+            servers: {
+                ...(existing.servers ?? {}),
+                ...makeMcpEntry(),
+            },
+        };
+        await fs.mkdir(path.dirname(configAbs), { recursive: true });
+        await fs.writeFile(configAbs, JSON.stringify(merged, null, 2) + "\n", "utf8");
+        results.push({
+            harness: harness.name,
+            configFile: harness.configFileRel,
+            action,
+        });
+    }
+    return results;
+}
+//# sourceMappingURL=mcp-install.js.map

package/dist/mcp-install.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server.d.ts

@@ -0,0 +1,7 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+/**
+ * Create a configured MCP server with all Commentray tools registered.
+ * @param repoRoot Absolute path to the Commentray project root
+ */
+export declare function createMcpServer(repoRoot: string): McpServer;
+//# sourceMappingURL=mcp-server.d.ts.map

package/dist/mcp-server.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server.js

@@ -0,0 +1,24 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { ALL_TOOLS } from "./mcp-tools.js";
+import serverPackage from "../package.json" with { type: "json" };
+/**
+ * Create a configured MCP server with all Commentray tools registered.
+ * @param repoRoot Absolute path to the Commentray project root
+ */
+export function createMcpServer(repoRoot) {
+    const server = new McpServer({
+        name: "commentray-mcp",
+        version: serverPackage.version,
+    });
+    for (const tool of ALL_TOOLS) {
+        registerTool(server, tool, repoRoot);
+    }
+    return server;
+}
+function registerTool(server, tool, repoRoot) {
+    // The MCP SDK infers args type from the schema; we pass through to our handler.
+    server.tool(tool.name, tool.description, tool.schema, async (args) => {
+        return tool.handler(repoRoot, args);
+    });
+}
+//# sourceMappingURL=mcp-server.js.map

package/dist/mcp-server.js.map

@@ -0,0 +1 @@
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package/dist/mcp-tools.d.ts

@@ -0,0 +1,17 @@
+import { z } from "zod";
+export interface McpToolDef {
+    name: string;
+    description: string;
+    schema: z.ZodRawShape;
+    handler: (repoRoot: string, args: Record<string, unknown>) => Promise<McpToolResult>;
+}
+export interface McpToolResult {
+    content: Array<{
+        type: "text";
+        text: string;
+    }>;
+    isError?: boolean;
+    [x: string]: unknown;
+}
+export declare const ALL_TOOLS: McpToolDef[];
+//# sourceMappingURL=mcp-tools.d.ts.map

package/dist/mcp-tools.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-tools.js

@@ -0,0 +1,574 @@
+import fs from "node:fs/promises";
+import path from "node:path";
+import { execSync } from "node:child_process";
+import { applyAnglesFlatMigrationToCommentrayToml, applyPathRenamesToCommentrayIndex, collectOrphanCompanionMarkdownTargets, convertCommentraySourceMarkersToLanguage, defaultMetadataIndexPath, discoverCommentrayPairsOnDisk, discoverFlatCompanionMarkdownFiles, ensureAnglesSentinelFile, GitScmProvider, initializeCommentrayProject, loadCommentrayConfig, normalizeRepoRelativePath, planAnglesMigrationFromCompanions, pruneOrphanCompanionMarkdown, readIndex, refreshIndexMigrationsOnDisk, resolveCommentrayMarkdownPath, rewriteIndexKeysForAnglesMigration, upsertAngleDefinitionInCommentrayToml, validateProject, writeIndex, } from "@commentray/core";
+import { renderSideBySideHtml } from "@commentray/render";
+import { z } from "zod";
+// ── Helpers ──────────────────────────────────────────────────────────────
+function textResult(text) {
+    return { content: [{ type: "text", text }] };
+}
+function errorResult(message) {
+    return { content: [{ type: "text", text: message }], isError: true };
+}
+// ── Tool definitions ─────────────────────────────────────────────────────
+export const ALL_TOOLS = [
+    // ── commentray_init ──────────────────────────────────────────────────
+    {
+        name: "commentray_init",
+        description: "Initialize a Commentray project in the current workspace. " +
+            "Creates the .commentray/ storage directory, index.json, and .commentray.toml " +
+            "configuration file. Idempotent — safe to run multiple times.",
+        schema: {},
+        handler: async (repoRoot) => {
+            const result = await initializeCommentrayProject(repoRoot);
+            const msgs = [];
+            if (result.createdToml)
+                msgs.push("Created .commentray.toml");
+            if (result.createdIndex)
+                msgs.push("Created index.json");
+            if (result.migratedIndex)
+                msgs.push("Migrated index to current schema");
+            if (result.addedSiteGitignore)
+                msgs.push("Added _site to .gitignore");
+            if (result.validationIssues.length > 0) {
+                for (const issue of result.validationIssues) {
+                    msgs.push(`[${issue.level.toUpperCase()}] ${issue.message}`);
+                }
+            }
+            if (msgs.length === 0)
+                msgs.push("Project already initialized (no changes).");
+            return textResult(msgs.join("\n"));
+        },
+    },
+    // ── commentray_validate ──────────────────────────────────────────────
+    {
+        name: "commentray_validate",
+        description: "Validate the Commentray project metadata and configuration. " +
+            "Returns errors and warnings. Set staged=true to only validate index entries " +
+            "touched by staged Git files.",
+        schema: {
+            staged: z.boolean().optional().default(false).describe("Only validate staged Git changes"),
+        },
+        handler: async (repoRoot, args) => {
+            const opts = args.staged
+                ? { stagedRepoRelativePaths: [] }
+                : undefined;
+            const result = await validateProject(repoRoot, opts);
+            const errors = result.issues.filter((i) => i.level === "error").length;
+            const warnings = result.issues.filter((i) => i.level === "warn").length;
+            const lines = [];
+            if (result.issues.length === 0) {
+                lines.push("OK: no validation issues.");
+            }
+            else {
+                for (const issue of result.issues) {
+                    lines.push(`[${issue.level.toUpperCase()}] ${issue.message}`);
+                }
+                lines.push("");
+                lines.push(`Summary: ${errors} error(s), ${warnings} warning(s)`);
+            }
+            return errors === 0 ? textResult(lines.join("\n")) : errorResult(lines.join("\n"));
+        },
+    },
+    // ── commentray_paths ─────────────────────────────────────────────────
+    {
+        name: "commentray_paths",
+        description: "Resolve and return the Commentray Markdown companion path for a source file. " +
+            "Given a repo-relative source file path, returns the corresponding .md path.",
+        schema: {
+            file: z.string().describe("Repo-relative path to the source file"),
+        },
+        handler: async (repoRoot, args) => {
+            const rel = normalizeRepoRelativePath(String(args.file));
+            const cfg = await loadCommentrayConfig(repoRoot);
+            const resolved = resolveCommentrayMarkdownPath(repoRoot, rel, cfg);
+            return textResult(resolved.commentrayPath);
+        },
+    },
+    // ── commentray_render ────────────────────────────────────────────────
+    {
+        name: "commentray_render",
+        description: "Render a side-by-side HTML page (source code + Commentray Markdown). " +
+            "Reads the source and markdown files from disk, writes HTML output.",
+        schema: {
+            source: z.string().optional().describe("Repo-relative source file path"),
+            markdown: z.string().optional().describe("Path to Commentray Markdown file"),
+            out: z.string().optional().default("_site/index.html").describe("Output HTML path"),
+            mermaid: z.boolean().optional().default(false).describe("Include Mermaid diagram runtime"),
+        },
+        handler: async (repoRoot, args) => {
+            const cfg = await loadCommentrayConfig(repoRoot);
+            const srcRel = args.source ?? cfg.staticSite?.sourceFile;
+            const mdRel = args.markdown ?? cfg.staticSite?.commentrayMarkdownFile;
+            const outRel = String(args.out ?? "_site/index.html");
+            if (!srcRel) {
+                return errorResult("No source file provided. Pass source or set [static_site].source_file in .commentray.toml.");
+            }
+            if (!mdRel) {
+                return errorResult("No markdown file provided. Pass markdown or set [static_site].commentray_markdown in .commentray.toml.");
+            }
+            const srcAbs = path.join(repoRoot, normalizeRepoRelativePath(String(srcRel)));
+            const mdAbs = path.join(repoRoot, normalizeRepoRelativePath(String(mdRel)));
+            const outAbs = path.resolve(repoRoot, outRel);
+            let code;
+            let mdText;
+            try {
+                code = await fs.readFile(srcAbs, "utf8");
+                mdText = await fs.readFile(mdAbs, "utf8");
+            }
+            catch (err) {
+                const codeErr = err.code;
+                if (codeErr === "ENOENT") {
+                    return errorResult("Source or markdown file not found. Check paths.");
+                }
+                throw err;
+            }
+            const ext = path.extname(String(srcRel)).slice(1) || "txt";
+            const html = await renderSideBySideHtml({
+                code,
+                language: ext,
+                commentrayMarkdown: mdText,
+                hljsTheme: cfg.render.syntaxTheme,
+                includeMermaidRuntime: Boolean(args.mermaid),
+            });
+            await fs.mkdir(path.dirname(outAbs), { recursive: true });
+            await fs.writeFile(outAbs, html, "utf8");
+            return textResult(`Rendered HTML to ${outRel}`);
+        },
+    },
+    // ── commentray_doctor ────────────────────────────────────────────────
+    {
+        name: "commentray_doctor",
+        description: "Run validation plus environment checks. With allowDeletions=true, also " +
+            "removes orphan companion Markdown files (no matching primary source file).",
+        schema: {
+            allowDeletions: z
+                .boolean()
+                .optional()
+                .default(false)
+                .describe("Remove orphan companion Markdown files"),
+        },
+        handler: async (repoRoot, args) => {
+            const lines = [];
+            if (args.allowDeletions) {
+                const cfg = await loadCommentrayConfig(repoRoot);
+                const { removedAbsPaths } = await pruneOrphanCompanionMarkdown(repoRoot, cfg.storageDir);
+                if (removedAbsPaths.length > 0) {
+                    lines.push(`Removed ${removedAbsPaths.length} orphan companion path(s):`);
+                    for (const abs of removedAbsPaths) {
+                        lines.push(`  - ${path.relative(repoRoot, abs)}`);
+                    }
+                }
+            }
+            const result = await validateProject(repoRoot);
+            const errors = result.issues.filter((i) => i.level === "error").length;
+            const warnings = result.issues.filter((i) => i.level === "warn").length;
+            if (result.issues.length === 0) {
+                lines.push("OK: no validation issues.");
+            }
+            else {
+                for (const issue of result.issues) {
+                    lines.push(`[${issue.level.toUpperCase()}] ${issue.message}`);
+                }
+                lines.push(`Summary: ${errors} error(s), ${warnings} warning(s)`);
+            }
+            try {
+                await fs.access(path.join(repoRoot, ".git"));
+                lines.push("OK: Git checkout detected.");
+            }
+            catch {
+                lines.push("[WARN] No .git directory — SCM features require a Git checkout.");
+            }
+            return errors === 0 ? textResult(lines.join("\n")) : errorResult(lines.join("\n"));
+        },
+    },
+    // ── commentray_migrate ───────────────────────────────────────────────
+    {
+        name: "commentray_migrate",
+        description: "Migrate the metadata index.json to the current schema version. " +
+            "Safe to run multiple times — only applies pending migrations.",
+        schema: {},
+        handler: async (repoRoot) => {
+            const { changed } = await refreshIndexMigrationsOnDisk(repoRoot);
+            if (changed) {
+                return textResult("Index migrated to current schema.");
+            }
+            return textResult("Index already at current schema (no migration needed).");
+        },
+    },
+    // ── commentray_migrate_angles ────────────────────────────────────────
+    {
+        name: "commentray_migrate_angles",
+        description: "Convert flat .commentray/source/ companions to the Angles layout " +
+            "(per-source folders under angle directories). Use dryRun=true to preview.",
+        schema: {
+            angleId: z.string().optional().default("main").describe("Angle ID for migrated files"),
+            dryRun: z.boolean().optional().default(false).describe("Preview moves without writing files"),
+        },
+        handler: async (repoRoot, args) => {
+            const cfg = await loadCommentrayConfig(repoRoot);
+            const storageDir = cfg.storageDir;
+            const companions = await discoverFlatCompanionMarkdownFiles(repoRoot, storageDir);
+            if (companions.length === 0) {
+                return textResult("No files to migrate (already in Angles layout or no flat companions).");
+            }
+            const angleId = String(args.angleId ?? "main");
+            const plan = planAnglesMigrationFromCompanions(companions, angleId, storageDir);
+            if (args.dryRun) {
+                const lines = [`Dry run: ${plan.moves.length} file(s) would be moved:`];
+                for (const m of plan.moves) {
+                    lines.push(`  ${m.fromRepoRel} → ${m.toRepoRel}`);
+                }
+                return textResult(lines.join("\n"));
+            }
+            // Apply filesystem moves
+            for (const m of plan.moves) {
+                const fromAbs = path.join(repoRoot, m.fromRepoRel);
+                const toAbs = path.join(repoRoot, m.toRepoRel);
+                await fs.mkdir(path.dirname(toAbs), { recursive: true });
+                await fs.rename(fromAbs, toAbs);
+            }
+            // Update .commentray.toml
+            const firstCompanion = companions[0];
+            const firstTarget = plan.moves[0];
+            const sourceFile = firstCompanion.sourcePath;
+            const fromCommentray = path.posix.join(storageDir, "source", `${sourceFile}.md`);
+            const toCommentray = firstTarget?.toRepoRel;
+            await applyAnglesFlatMigrationToCommentrayToml(repoRoot, {
+                angleId,
+                staticCommentrayMarkdownFrom: fromCommentray,
+                staticCommentrayMarkdownTo: toCommentray,
+            });
+            // Rewrite index keys
+            const index = await readIndex(repoRoot);
+            if (index) {
+                const newIndex = rewriteIndexKeysForAnglesMigration(index, plan.flatToAnglePath);
+                await writeIndex(repoRoot, newIndex);
+            }
+            return textResult(`Migrated ${plan.moves.length} file(s) to angle "${angleId}".`);
+        },
+    },
+    // ── commentray_angles_add ────────────────────────────────────────────
+    {
+        name: "commentray_angles_add",
+        description: "Register a new angle in .commentray.toml and create the Angles sentinel. " +
+            "Use makeDefault=true to set it as the default angle.",
+        schema: {
+            angleId: z
+                .string()
+                .regex(/^[a-zA-Z0-9_-]+$/)
+                .describe("New angle ID (letters, digits, underscores, hyphens)"),
+            source: z.string().optional().describe("Repo-relative primary source path"),
+            title: z.string().optional().describe("Human-readable angle label"),
+            makeDefault: z.boolean().optional().default(false).describe("Set as the default angle"),
+        },
+        handler: async (repoRoot, args) => {
+            await upsertAngleDefinitionInCommentrayToml(repoRoot, {
+                id: String(args.angleId),
+                title: args.title ? String(args.title) : undefined,
+                makeDefault: Boolean(args.makeDefault),
+            });
+            const cfg = await loadCommentrayConfig(repoRoot);
+            await ensureAnglesSentinelFile(repoRoot, cfg.storageDir);
+            return textResult(`Angle "${args.angleId}" registered${args.makeDefault ? " (default)" : ""}.`);
+        },
+    },
+    // ── commentray_sync_moved_paths ──────────────────────────────────────
+    {
+        name: "commentray_sync_moved_paths",
+        description: "Rewrite index.json paths using Git rename detection between two tree-ish refs. " +
+            "Use dryRun=true to preview without writing.",
+        schema: {
+            from: z.string().optional().default("HEAD~1").describe("Older tree-ish ref"),
+            to: z.string().optional().default("HEAD").describe("Newer tree-ish ref"),
+            dryRun: z.boolean().optional().default(false).describe("Preview renames without writing"),
+        },
+        handler: async (repoRoot, args) => {
+            const scm = new GitScmProvider();
+            if (!scm.listPathRenamesBetweenTreeishes) {
+                return errorResult("SCM provider does not support rename listing.");
+            }
+            const fromRef = String(args.from ?? "HEAD~1");
+            const toRef = String(args.to ?? "HEAD");
+            const renames = await scm.listPathRenamesBetweenTreeishes(repoRoot, fromRef, toRef);
+            if (renames.length === 0) {
+                return textResult("No Git-detected renames in that range.");
+            }
+            const cfg = await loadCommentrayConfig(repoRoot);
+            const index = await readIndex(repoRoot);
+            if (!index) {
+                return errorResult(`No index at ${defaultMetadataIndexPath()}. Run commentray_init first.`);
+            }
+            const next = applyPathRenamesToCommentrayIndex(index, renames, repoRoot, cfg);
+            if (!next.changed) {
+                return textResult("Index paths already match those renames (nothing to update).");
+            }
+            if (args.dryRun) {
+                const lines = [`Dry run: would apply ${renames.length} rename(s):`];
+                for (const r of renames) {
+                    lines.push(`  ${r.from} → ${r.to}`);
+                }
+                return textResult(lines.join("\n"));
+            }
+            await writeIndex(repoRoot, next.index);
+            return textResult(`Applied ${renames.length} rename(s) to index.json.`);
+        },
+    },
+    // ── commentray_convert_source_markers ────────────────────────────────
+    {
+        name: "commentray_convert_source_markers",
+        description: "Rewrite Commentray marker pairs in a source file to the delimiter style " +
+            "for a given VS Code language ID. Use dryRun=true to preview.",
+        schema: {
+            file: z.string().describe("Repo-relative path to the source file"),
+            language: z.string().describe("VS Code language ID (e.g. typescript, rust, yaml, css)"),
+            dryRun: z
+                .boolean()
+                .optional()
+                .default(false)
+                .describe("Preview changes without writing the file"),
+        },
+        handler: async (repoRoot, args) => {
+            const rel = normalizeRepoRelativePath(String(args.file));
+            const abs = path.join(repoRoot, ...rel.split("/"));
+            let raw;
+            try {
+                raw = await fs.readFile(abs, "utf8");
+            }
+            catch (err) {
+                const code = err.code;
+                if (code === "ENOENT")
+                    return errorResult(`File not found: ${rel}`);
+                throw err;
+            }
+            const { sourceText, changed, convertedPairs } = convertCommentraySourceMarkersToLanguage(raw, String(args.language));
+            if (!changed) {
+                return textResult("No changes (no marker pairs, already target style, or only line-ending normalization).");
+            }
+            if (args.dryRun) {
+                return textResult(`Dry run: would rewrite ${convertedPairs} marker pair(s) in ${rel}.`);
+            }
+            await fs.writeFile(abs, sourceText, "utf8");
+            return textResult(`Rewrote ${convertedPairs} marker pair(s) in ${rel}.`);
+        },
+    },
+    // ── Read-only discovery tools ────────────────────────────────────────
+    {
+        name: "commentray_list_pairs",
+        description: "List all source→commentary pairs in the project. " +
+            "Returns repo-relative paths for each source file and its companion Markdown. " +
+            "Use this to discover what files already have commentary.",
+        schema: {},
+        handler: async (repoRoot) => {
+            const cfg = await loadCommentrayConfig(repoRoot);
+            const pairs = await discoverCommentrayPairsOnDisk(repoRoot, cfg.storageDir);
+            if (pairs.length === 0) {
+                return textResult("No commentray pairs found. Run commentray_init first, then add commentary.");
+            }
+            const lines = [`${pairs.length} source→commentary pair(s):`];
+            for (const p of pairs) {
+                lines.push(`  ${p.sourcePath}  →  ${p.commentrayPath}`);
+            }
+            return textResult(lines.join("\n"));
+        },
+    },
+    {
+        name: "commentray_read_commentray",
+        description: "Read the commentary Markdown for a given source file. " +
+            "Returns the full Markdown content. Use this before writing or editing commentary.",
+        schema: {
+            file: z.string().describe("Repo-relative path to the source file"),
+            angleId: z.string().optional().describe("Angle ID (uses default if omitted)"),
+        },
+        handler: async (repoRoot, args) => {
+            const rel = normalizeRepoRelativePath(String(args.file));
+            const cfg = await loadCommentrayConfig(repoRoot);
+            const resolved = resolveCommentrayMarkdownPath(repoRoot, rel, cfg, args.angleId ? String(args.angleId) : undefined);
+            const absPath = path.join(repoRoot, ...resolved.commentrayPath.split("/"));
+            try {
+                const content = await fs.readFile(absPath, "utf8");
+                return textResult(content);
+            }
+            catch (err) {
+                const code = err.code;
+                if (code === "ENOENT") {
+                    return errorResult(`No commentary found for ${rel}. Run commentray_init and add commentary first.`);
+                }
+                throw err;
+            }
+        },
+    },
+    {
+        name: "commentray_read_source",
+        description: "Read a source file's content. Returns the full file text. " +
+            "Use this to understand the code before writing commentary for it.",
+        schema: {
+            file: z.string().describe("Repo-relative path to the source file"),
+        },
+        handler: async (repoRoot, args) => {
+            const rel = normalizeRepoRelativePath(String(args.file));
+            const abs = path.join(repoRoot, ...rel.split("/"));
+            try {
+                const content = await fs.readFile(abs, "utf8");
+                const lines = content.split("\n");
+                const header = `// ${rel}  (${lines.length} lines, ${content.length} bytes)\n`;
+                return textResult(header + content);
+            }
+            catch (err) {
+                const code = err.code;
+                if (code === "ENOENT")
+                    return errorResult(`File not found: ${rel}`);
+                throw err;
+            }
+        },
+    },
+    {
+        name: "commentray_list_orphans",
+        description: "List orphan companion Markdown files — commentary without a matching " +
+            "primary source file. Use commentray_doctor with allowDeletions=true to remove them.",
+        schema: {},
+        handler: async (repoRoot) => {
+            const cfg = await loadCommentrayConfig(repoRoot);
+            const orphans = await collectOrphanCompanionMarkdownTargets(repoRoot, cfg.storageDir);
+            if (orphans.length === 0) {
+                return textResult("No orphan companions found. All commentary files have matching source files.");
+            }
+            const lines = [`${orphans.length} orphan companion(s) found:`];
+            for (const o of orphans) {
+                const kind = o.cleanupIsDirectory ? "dir" : "file";
+                lines.push(`  [${kind}] ${o.commentrayPath}  (missing source: ${o.sourcePath})`);
+            }
+            lines.push("");
+            lines.push("To remove them: use commentray_doctor with allowDeletions=true, or run `commentray doctor --allow-deletions` from the CLI.");
+            return textResult(lines.join("\n"));
+        },
+    },
+    {
+        name: "commentray_find_uncommented",
+        description: "Find source files in the repo that could have commentary but don't. " +
+            "Scans Git-tracked files, filters by common source extensions, and " +
+            "compares against the index. Use this to discover documentation opportunities.",
+        schema: {
+            maxFiles: z
+                .number()
+                .optional()
+                .default(100)
+                .describe("Maximum files to return (prevents overwhelming output)"),
+        },
+        handler: async (repoRoot, args) => {
+            // Get git-tracked files
+            let tracked;
+            try {
+                tracked = execSync("git ls-files -z --cached", {
+                    cwd: repoRoot,
+                    encoding: "utf8",
+                    maxBuffer: 10 * 1024 * 1024,
+                });
+            }
+            catch {
+                return errorResult("Could not list Git-tracked files. Ensure the repo has a Git checkout and git is on PATH.");
+            }
+            const allFiles = tracked.split("\0").filter(Boolean);
+            const sourceExts = new Set([
+                ".ts",
+                ".tsx",
+                ".js",
+                ".jsx",
+                ".py",
+                ".rs",
+                ".go",
+                ".java",
+                ".kt",
+                ".swift",
+                ".c",
+                ".cpp",
+                ".h",
+                ".hpp",
+                ".cs",
+                ".rb",
+                ".php",
+                ".scala",
+                ".clj",
+                ".ex",
+                ".exs",
+                ".elm",
+                ".hs",
+                ".lua",
+                ".r",
+                ".nim",
+                ".zig",
+                ".ml",
+                ".mli",
+                ".yaml",
+                ".yml",
+                ".toml",
+                ".json",
+                ".md",
+                ".mdx",
+            ]);
+            const index = await readIndex(repoRoot);
+            const indexedPaths = new Set();
+            if (index) {
+                for (const entry of Object.values(index.byCommentrayPath)) {
+                    indexedPaths.add(entry.sourcePath);
+                }
+            }
+            const uncommented = [];
+            for (const f of allFiles) {
+                const ext = path.extname(f).toLowerCase();
+                if (!sourceExts.has(ext))
+                    continue;
+                if (indexedPaths.has(f))
+                    continue;
+                uncommented.push(f);
+                if (uncommented.length >= args.maxFiles)
+                    break;
+            }
+            const totalSource = allFiles.filter((f) => sourceExts.has(path.extname(f).toLowerCase())).length;
+            const commented = totalSource - uncommented.length;
+            if (uncommented.length === 0) {
+                return textResult(`All ${totalSource} tracked source files have commentary. Great job!`);
+            }
+            const lines = [
+                `${uncommented.length} uncommented source file(s) (${commented} already have commentary, ${totalSource} total tracked source files):`,
+            ];
+            for (const f of uncommented) {
+                lines.push(`  ${f}`);
+            }
+            if (uncommented.length >= args.maxFiles) {
+                lines.push(`  ... (capped at ${args.maxFiles}; increase maxFiles to see more)`);
+            }
+            return textResult(lines.join("\n"));
+        },
+    },
+    {
+        name: "commentray_get_index",
+        description: "Return the full Commentray index as formatted JSON. " +
+            "Shows all tracked source files, their companion paths, block IDs, anchors, and marker IDs. " +
+            "Use this to understand the complete state of the project's commentary.",
+        schema: {},
+        handler: async (repoRoot) => {
+            const index = await readIndex(repoRoot);
+            if (!index) {
+                return errorResult(`No index found. Run commentray_init first.`);
+            }
+            const summary = {
+                schemaVersion: index.schemaVersion,
+                pairCount: Object.keys(index.byCommentrayPath).length,
+                pairs: Object.entries(index.byCommentrayPath).map(([cp, entry]) => ({
+                    sourcePath: entry.sourcePath,
+                    commentrayPath: cp,
+                    blockCount: entry.blocks.length,
+                    blocks: entry.blocks.map((b) => ({
+                        id: b.id,
+                        anchor: b.anchor,
+                        markerId: b.markerId,
+                    })),
+                })),
+            };
+            return textResult(JSON.stringify(summary, null, 2));
+        },
+    },
+];
+//# sourceMappingURL=mcp-tools.js.map

package/dist/mcp-tools.js.map

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package/dist/repo-root.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Walk up from `cwd` looking for a Commentray project root.
+ * Checks for `.commentray.toml` first, then `.git` as fallback.
+ * Returns `cwd` if nothing found.
+ */
+export declare function repoRootFrom(cwd: string): Promise<string>;
+//# sourceMappingURL=repo-root.d.ts.map

package/dist/repo-root.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"repo-root.d.ts","sourceRoot":"","sources":["../src/repo-root.ts"],"names":[],"mappings":"AAGA;;;;GAIG;AACH,wBAAsB,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAoB/D"}

package/dist/repo-root.js

@@ -0,0 +1,32 @@
+import fs from "node:fs/promises";
+import path from "node:path";
+/**
+ * Walk up from `cwd` looking for a Commentray project root.
+ * Checks for `.commentray.toml` first, then `.git` as fallback.
+ * Returns `cwd` if nothing found.
+ */
+export async function repoRootFrom(cwd) {
+    let current = path.resolve(cwd);
+    for (;;) {
+        try {
+            await fs.access(path.join(current, ".commentray.toml"));
+            return current;
+        }
+        catch {
+            // not found
+        }
+        try {
+            await fs.access(path.join(current, ".git"));
+            return current;
+        }
+        catch {
+            // not found
+        }
+        const parent = path.dirname(current);
+        if (parent === current)
+            break;
+        current = parent;
+    }
+    return path.resolve(cwd);
+}
+//# sourceMappingURL=repo-root.js.map

package/dist/repo-root.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"repo-root.js","sourceRoot":"","sources":["../src/repo-root.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAClC,OAAO,IAAI,MAAM,WAAW,CAAC;AAE7B;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,GAAW;IAC5C,IAAI,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;IAChC,SAAS,CAAC;QACR,IAAI,CAAC;YACH,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,kBAAkB,CAAC,CAAC,CAAC;YACxD,OAAO,OAAO,CAAC;QACjB,CAAC;QAAC,MAAM,CAAC;YACP,YAAY;QACd,CAAC;QACD,IAAI,CAAC;YACH,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC,CAAC;YAC5C,OAAO,OAAO,CAAC;QACjB,CAAC;QAAC,MAAM,CAAC;YACP,YAAY;QACd,CAAC;QACD,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QACrC,IAAI,MAAM,KAAK,OAAO;YAAE,MAAM;QAC9B,OAAO,GAAG,MAAM,CAAC;IACnB,CAAC;IACD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;AAC3B,CAAC"}

package/dist/stdio-entry.d.ts

@@ -0,0 +1,13 @@
+#!/usr/bin/env node
+/**
+ * MCP server entry point — stdio transport.
+ *
+ * Connect an MCP client (Claude Desktop, VS Code Copilot, etc.) by configuring
+ * it to run this script with the Commentray project root as the working directory.
+ *
+ * Usage:
+ *   node dist/stdio-entry.js          (from within a Commentray project)
+ *   commentray mcp serve              (CLI wrapper)
+ */
+export {};
+//# sourceMappingURL=stdio-entry.d.ts.map

package/dist/stdio-entry.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"stdio-entry.d.ts","sourceRoot":"","sources":["../src/stdio-entry.ts"],"names":[],"mappings":";AACA;;;;;;;;;GASG"}

package/dist/stdio-entry.js

@@ -0,0 +1,25 @@
+#!/usr/bin/env node
+/**
+ * MCP server entry point — stdio transport.
+ *
+ * Connect an MCP client (Claude Desktop, VS Code Copilot, etc.) by configuring
+ * it to run this script with the Commentray project root as the working directory.
+ *
+ * Usage:
+ *   node dist/stdio-entry.js          (from within a Commentray project)
+ *   commentray mcp serve              (CLI wrapper)
+ */
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { createMcpServer } from "./mcp-server.js";
+import { repoRootFrom } from "./repo-root.js";
+async function main() {
+    const repoRoot = await repoRootFrom(process.cwd());
+    const server = createMcpServer(repoRoot);
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+}
+main().catch((err) => {
+    console.error("commentray-mcp: fatal error during startup:", err);
+    process.exit(1);
+});
+//# sourceMappingURL=stdio-entry.js.map

package/dist/stdio-entry.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"stdio-entry.js","sourceRoot":"","sources":["../src/stdio-entry.ts"],"names":[],"mappings":";AACA;;;;;;;;;GASG;AAEH,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,eAAe,EAAE,MAAM,iBAAiB,CAAC;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAE9C,KAAK,UAAU,IAAI;IACjB,MAAM,QAAQ,GAAG,MAAM,YAAY,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC;IACnD,MAAM,MAAM,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;IACzC,MAAM,SAAS,GAAG,IAAI,oBAAoB,EAAE,CAAC;IAC7C,MAAM,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;AAClC,CAAC;AAED,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,EAAE;IACnB,OAAO,CAAC,KAAK,CAAC,6CAA6C,EAAE,GAAG,CAAC,CAAC;IAClE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC"}

package/dist/test/test-helpers.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Create a temporary directory with a minimal Commentray project.
+ * Writes .commentray.toml, initializes index.json, creates a sample source file.
+ * Returns the repo root path and the source file relative path.
+ */
+export declare function setupTempCommentrayProject(): Promise<{
+    repoRoot: string;
+    sourceRel: string;
+    cleanup: () => Promise<void>;
+}>;
+//# sourceMappingURL=test-helpers.d.ts.map

package/dist/test/test-helpers.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"test-helpers.d.ts","sourceRoot":"","sources":["../../src/test/test-helpers.ts"],"names":[],"mappings":"AAIA;;;;GAIG;AACH,wBAAsB,0BAA0B,IAAI,OAAO,CAAC;IAC1D,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,OAAO,CAAC,IAAI,CAAC,CAAC;CAC9B,CAAC,CAkCD"}

package/dist/test/test-helpers.js

@@ -0,0 +1,26 @@
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+/**
+ * Create a temporary directory with a minimal Commentray project.
+ * Writes .commentray.toml, initializes index.json, creates a sample source file.
+ * Returns the repo root path and the source file relative path.
+ */
+export async function setupTempCommentrayProject() {
+    const repoRoot = await fs.mkdtemp(path.join(os.tmpdir(), "commentray-mcp-test-"));
+    const sourceRel = "src/example.ts";
+    // Create dirs
+    await fs.mkdir(path.join(repoRoot, "src"), { recursive: true });
+    await fs.mkdir(path.join(repoRoot, ".commentray", "metadata"), { recursive: true });
+    // Write .commentray.toml
+    await fs.writeFile(path.join(repoRoot, ".commentray.toml"), ["[storage]", 'dir = ".commentray"', "", "[scm]", 'provider = "git"', ""].join("\n"), "utf8");
+    // Write index.json (empty, current schema)
+    await fs.writeFile(path.join(repoRoot, ".commentray", "metadata", "index.json"), JSON.stringify({ schemaVersion: 3, byCommentrayPath: {} }), "utf8");
+    // Write sample source file
+    await fs.writeFile(path.join(repoRoot, sourceRel), "// example.ts\n\nexport function hello(): string {\n  return 'hello';\n}\n", "utf8");
+    const cleanup = async () => {
+        await fs.rm(repoRoot, { recursive: true, force: true });
+    };
+    return { repoRoot, sourceRel, cleanup };
+}
+//# sourceMappingURL=test-helpers.js.map

package/dist/test/test-helpers.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"test-helpers.js","sourceRoot":"","sources":["../../src/test/test-helpers.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAClC,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAE7B;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,0BAA0B;IAK9C,MAAM,QAAQ,GAAG,MAAM,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,sBAAsB,CAAC,CAAC,CAAC;IAClF,MAAM,SAAS,GAAG,gBAAgB,CAAC;IAEnC,cAAc;IACd,MAAM,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAChE,MAAM,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,aAAa,EAAE,UAAU,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAEpF,yBAAyB;IACzB,MAAM,EAAE,CAAC,SAAS,CAChB,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,kBAAkB,CAAC,EACvC,CAAC,WAAW,EAAE,qBAAqB,EAAE,EAAE,EAAE,OAAO,EAAE,kBAAkB,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EACpF,MAAM,CACP,CAAC;IAEF,2CAA2C;IAC3C,MAAM,EAAE,CAAC,SAAS,CAChB,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,aAAa,EAAE,UAAU,EAAE,YAAY,CAAC,EAC5D,IAAI,CAAC,SAAS,CAAC,EAAE,aAAa,EAAE,CAAC,EAAE,gBAAgB,EAAE,EAAE,EAAE,CAAC,EAC1D,MAAM,CACP,CAAC;IAEF,2BAA2B;IAC3B,MAAM,EAAE,CAAC,SAAS,CAChB,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,CAAC,EAC9B,4EAA4E,EAC5E,MAAM,CACP,CAAC;IAEF,MAAM,OAAO,GAAG,KAAK,IAAI,EAAE;QACzB,MAAM,EAAE,CAAC,EAAE,CAAC,QAAQ,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;IAC1D,CAAC,CAAC;IAEF,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,OAAO,EAAE,CAAC;AAC1C,CAAC"}

package/package.json

@@ -0,0 +1,36 @@
+{
+  "name": "@commentray/mcp-server",
+  "version": "0.4.1",
+  "publishConfig": {
+    "access": "public"
+  },
+  "description": "MCP (Model Context Protocol) server for Commentray — exposes CLI commands as AI coding assistant tools",
+  "license": "MPL-2.0",
+  "type": "module",
+  "sideEffects": false,
+  "main": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js"
+    }
+  },
+  "files": [
+    "dist",
+    "LICENSE"
+  ],
+  "scripts": {
+    "build": "tsc -p tsconfig.build.json",
+    "clean": "rm -rf dist"
+  },
+  "dependencies": {
+    "@commentray/core": "0.3.6",
+    "@commentray/render": "0.3.6",
+    "@modelcontextprotocol/sdk": "^1.29.0",
+    "zod": "^4.4.3"
+  },
+  "devDependencies": {
+    "@types/node": "^26.0.1"
+  }
+}