@sudosandwich/limps 2.6.1 → 2.8.0

package/README.md

@@ -270,7 +270,7 @@ Config location varies by OS:
   "docsPaths": ["~/Documents/my-plans"],
   "fileExtensions": [".md"],
   "dataPath": "~/Library/Application Support/limps/data",
-  "extensions": ["@sudosandwich/limps-radix"],
+  "extensions": ["@sudosandwich/limps-headless"],
   "scoring": {
     "weights": { "dependency": 40, "priority": 30, "workload": 30 },
     "biases": {}
@@ -302,23 +302,23 @@ limps exposes 15 MCP tools for AI assistants:
 Extensions add MCP tools and resources. Install from npm:
 
 ```bash
-npm install -g @sudosandwich/limps-radix
+npm install -g @sudosandwich/limps-headless
 ```
 
 Add to config:
 
 ```json
 {
-  "extensions": ["@sudosandwich/limps-radix"],
-  "@sudosandwich/limps-radix": {
-    "cacheDir": "~/Library/Application Support/limps-radix"
+  "extensions": ["@sudosandwich/limps-headless"],
+  "limps-headless": {
+    "cacheDir": "~/Library/Application Support/limps-headless"
   }
 }
 ```
 
 **Available extensions:**
 
-- `@sudosandwich/limps-radix` — Radix UI contract extraction and semantic analysis
+- `@sudosandwich/limps-headless` — Headless UI contract extraction, semantic analysis, and drift detection (Radix UI and Base UI migration).
 
 ## Obsidian Compatibility
 
@@ -343,7 +343,7 @@ npm test
 This is a monorepo with:
 
 - `packages/limps` — Core MCP server
-- `packages/limps-radix` — Radix UI extension
+- `packages/limps-headless` — Headless UI extension (Radix/Base UI contract extraction and audit)
 
 ## Used in Production
 
@@ -380,7 +380,7 @@ NNNN-descriptive-name/
 
 ### Why the prefixes?
 
-I chose this to keep things lexicographically ordered and easier to reference in chat. "Show me the next agent or agents we can run now in plan 25", and the MCP will run the tool to process the agents applying weights and biases to choose the next best task or tasks that can run in parallel.
+I chose this to keep things lexicographically ordered and easier to reference in chat. "Show me the next agent or agents we can run now in plan NNNN-plan-name", and the MCP will run the tool to process the agents applying weights and biases to choose the next best task or tasks that can run in parallel.
 
 ## Deep Dive
 
@@ -490,7 +490,6 @@ Progressive disclosure via resources:
 | `plans://summary` | Plan summaries with key info |
 | `plans://full` | Full plan documents |
 | `decisions://log` | Decision log entries |
-| `agents://status` | Agent status and tasks |
 
 </details>
 

package/dist/cli/config-cmd.d.ts

@@ -28,6 +28,8 @@ export declare function getProjectsData(): ProjectsData;
 export declare function configList(): string;
 /**
  * Switch to a different project.
+ * If the name is not in the registry but exists in the default discovery location
+ * (Application Support/<name>/config.json), registers it and sets as current.
  *
  * @param name - Project name to switch to
  * @returns Success message
@@ -80,14 +82,16 @@ export declare function configPath(resolveConfigPathFn: () => string): string;
  */
 export declare function configAdd(name: string, configFileOrDirPath: string): string;
 /**
- * Remove a project from the registry.
- * Does not delete any files.
+ * Remove a project from the registry and delete its config file and project directory
+ * when the config lives under limps/projects (Application Support/limps/projects/).
+ * Accepts either a project name (exact match, no path chars) or a path to a config file.
+ * Paths are strictly validated: must be under limps/projects and end with config.json.
  *
- * @param name - Project name to remove
+ * @param nameOrPath - Project name or path to config.json
  * @returns Success message
- * @throws Error if project not found
+ * @throws Error if project not found or path is invalid
  */
-export declare function configRemove(name: string): string;
+export declare function configRemove(nameOrPath: string): string;
 /**
  * Set the current project from an existing config file path.
  * Auto-derives the project name from the parent directory.
@@ -100,12 +104,29 @@ export declare function configRemove(name: string): string;
 export declare function configSet(configFilePath: string): string;
 import { LocalMcpAdapter, type McpClientAdapter, type McpServerConfig } from './mcp-client-adapter.js';
 /**
- * Discover and register config files from default OS locations.
- * Scans the OS-specific application support directories for config.json files.
+ * Discover config files under limps/projects (Application Support/limps/projects/<name>/config.json).
+ * Does not auto-register; use `limps config use <name>` to register and switch.
  *
- * @returns Summary of discovered projects
+ * @returns Summary of discovered (unregistered) projects
  */
 export declare function configDiscover(): string;
+/**
+ * Migrate known (registered) configs and configs from old locations into limps/projects/
+ * so the limps root is not polluted. Ensures limps/projects exists, then:
+ * 1. For each registered project: if config is not under limps/projects/<name>/, copy it there and update registry.
+ * 2. Pull from old sibling layout (Application Support/<name>/config.json): copy to limps/projects/<name>/, register.
+ * 3. Pull from flat limps layout (limps/<name>/config.json): copy to limps/projects/<name>/, register if not already.
+ * Repairs all paths inside each config JSON (plansPath, dataPath, docsPaths) and MCP client references.
+ *
+ * @returns Summary of migration (migrated count and paths)
+ */
+/** One recorded move for migration reversal. */
+export interface MigrationMove {
+    name: string;
+    sourcePath: string;
+    targetPath: string;
+}
+export declare function configMigrate(): string;
 /**
  * Generate MCP server configuration JSON for limps projects.
  * Returns the JSON structure that should be added to the client config.

package/dist/cli/config-cmd.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"config-cmd.d.ts","sourceRoot":"","sources":["../../src/cli/config-cmd.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAmCH;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,QAAQ,EAAE;QACR,IAAI,EAAE,MAAM,CAAC;QACb,UAAU,EAAE,MAAM,CAAC;QACnB,OAAO,EAAE,OAAO,CAAC;QACjB,MAAM,EAAE,OAAO,CAAC;KACjB,EAAE,CAAC;IACJ,KAAK,EAAE,MAAM,CAAC;CACf;AAED;;;;GAIG;AACH,wBAAgB,eAAe,IAAI,YAAY,CAY9C;AAED;;;;GAIG;AACH,wBAAgB,UAAU,IAAI,MAAM,CAmBnC;AAED;;;;;;;;GAQG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CA6B9C;AAED;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE;QACN,SAAS,EAAE,MAAM,CAAC;QAClB,QAAQ,EAAE,MAAM,CAAC;QACjB,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;QACrB,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;KAC3B,CAAC;CACH;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,mBAAmB,EAAE,MAAM,MAAM,GAAG,UAAU,CAkB3E;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,mBAAmB,EAAE,MAAM,MAAM,GAAG,MAAM,CA0FpE;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,mBAAmB,EAAE,MAAM,MAAM,GAAG,MAAM,CAEpE;AAED;;;;;;;;;GASG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,mBAAmB,EAAE,MAAM,GAAG,MAAM,CAqF3E;AA+BD;;;;;;;;;GASG;AACH,wBAAgB,YAAY,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CA+FvD;AAED;;;;;;;;GAQG;AACH,wBAAgB,SAAS,CAAC,cAAc,EAAE,MAAM,GAAG,MAAM,CAmCxD;AAED,OAAO,EAEL,eAAe,EAEf,KAAK,gBAAgB,EAErB,KAAK,eAAe,EACrB,MAAM,yBAAyB,CAAC;AAEjC;;;;;GAKG;AACH,wBAAgB,cAAc,IAAI,MAAM,CAkDvC;AAwFD;;;;;;;;;GASG;AACH,gDAAgD;AAChD,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;CACpB;AAyBD,wBAAgB,aAAa,IAAI,MAAM,CAsItC;AAED;;;;;;;;;GASG;AACH,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,gBAAgB,EACzB,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB;IACD,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC;IACzC,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACrC,CAuEA;AAqGD;;;GAGG;AACH,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,gBAAgB,EACzB,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB;IACD,UAAU,EAAE,OAAO,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,UAAU,EAAE,MAAM,CAAC;CACpB,CAoDA;AAuED;;;;;;;GAOG;AACH,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,gBAAgB,EACzB,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB,MAAM,CAoBR;AAED;;;;;;;;;GASG;AACH,wBAAgB,eAAe,CAC7B,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB,MAAM,CAGR;AAED;;;;;;;;;GASG;AACH,wBAAgB,eAAe,CAC7B,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB,MAAM,CAGR;AAED;;;;;;;;;GASG;AACH,wBAAgB,mBAAmB,CACjC,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB,MAAM,CAGR;AAED;;;;;;;;;GASG;AACH,wBAAgB,cAAc,CAC5B,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB,MAAM,CAGR;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,iBAAiB,CAC/B,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,EACxB,aAAa,CAAC,EAAE,eAAe,GAAG,MAAM,GACvC,MAAM,CAWR;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,OAAO,CAG7D;AAED;;;;;;;GAOG;AACH,wBAAgB,2BAA2B,CACzC,mBAAmB,EAAE,MAAM,MAAM,EACjC,aAAa,CAAC,EAAE,MAAM,EAAE,GACvB,MAAM,CAkDR;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;GAQG;AACH,wBAAgB,YAAY,CAAC,WAAW,EAAE,MAAM,EAAE,OAAO,EAAE,mBAAmB,GAAG,MAAM,CAgDtF"}

package/dist/cli/config-cmd.js

@@ -2,13 +2,21 @@
  * Config subcommand handlers for limps CLI.
  * Provides commands to manage the project registry and view configuration.
  */
-import { existsSync, readdirSync, readFileSync, writeFileSync, statSync, mkdirSync } from 'fs';
+import { existsSync, readdirSync, readFileSync, writeFileSync, statSync, mkdirSync, realpathSync, rmSync, } from 'fs';
 import * as jsonpatch from 'fast-json-patch';
-import { resolve, dirname, basename, join } from 'path';
+import { resolve, dirname, basename, join, relative, sep } from 'path';
 import * as toml from '@iarna/toml';
 import { registerProject, unregisterProject, setCurrentProject, listProjects, loadRegistry, } from './registry.js';
-import { loadConfig } from '../config.js';
-import { getOSBasePath, getOSConfigPath, getOSDataPath } from '../utils/os-paths.js';
+import { loadConfig, validateConfig } from '../config.js';
+import { getOSBasePath } from '../utils/os-paths.js';
+/** Child dir under limps for project configs (limps/projects/<name>/config.json). */
+const PROJECTS_DIR = 'projects';
+/**
+ * Root directory for project configs under limps (Application Support/limps/projects/).
+ */
+function getProjectsRoot() {
+    return join(getOSBasePath('limps'), PROJECTS_DIR);
+}
 /**
  * Get projects data for JSON output.
  *
@@ -49,14 +57,39 @@ export function configList() {
 }
 /**
  * Switch to a different project.
+ * If the name is not in the registry but exists in the default discovery location
+ * (Application Support/<name>/config.json), registers it and sets as current.
  *
  * @param name - Project name to switch to
  * @returns Success message
  * @throws Error if project not found
  */
 export function configUse(name) {
-    setCurrentProject(name);
-    return `Switched to project "${name}"`;
+    if (!name || !SAFE_NAME_REGEX.test(name)) {
+        throw new Error(`Invalid project name: must not be empty and must not contain path separators.\nRun \`limps config list\` to see available projects.`);
+    }
+    const registry = loadRegistry();
+    if (registry.projects[name]) {
+        setCurrentProject(name);
+        return `Switched to project "${name}"`;
+    }
+    // Not registered: try default discovery location so "discover" + "use <name>" works
+    const searchDir = getProjectsRoot();
+    const configPath = join(searchDir, name, 'config.json');
+    if (existsSync(configPath)) {
+        try {
+            const raw = JSON.parse(readFileSync(configPath, 'utf-8'));
+            if (validateConfig(raw)) {
+                registerProject(name, configPath);
+                setCurrentProject(name);
+                return `Registered and switched to project "${name}"`;
+            }
+        }
+        catch {
+            // Not valid JSON or not a limps config, fall through to throw
+        }
+    }
+    throw new Error(`Project not found: ${name}\nRun \`limps config list\` to see available projects.`);
 }
 /**
  * Get configuration data for JSON output.
@@ -204,10 +237,10 @@ export function configAdd(name, configFileOrDirPath) {
             registerProject(name, configInDir);
             return `Registered project "${name}" with config: ${configInDir}`;
         }
-        // No config.json found - create one in OS standard location
-        const basePath = getOSBasePath(name);
-        const configPath = getOSConfigPath(name);
-        const dataPath = getOSDataPath(name);
+        // No config.json found - create one under limps/projects/<name>/
+        const basePath = join(getProjectsRoot(), name);
+        const configPath = join(basePath, 'config.json');
+        const dataPath = join(basePath, 'data');
         // Check if config already exists in OS location
         if (existsSync(configPath)) {
             throw new Error(`Config already exists at: ${configPath}\nTo reconfigure, delete the existing config file first.`);
@@ -253,17 +286,116 @@ export function configAdd(name, configFileOrDirPath) {
     registerProject(name, absolutePath);
     return `Registered project "${name}" with config: ${absolutePath}`;
 }
+/** Project names must not contain path separators or traversal (prompt injection / misuse). */
+const SAFE_NAME_REGEX = /^[^/\\]+$/;
+/**
+ * Delete the config file and its project directory when under discovery root.
+ * Only deletes when the config path is under discovery root (application config directory).
+ */
+function deleteConfigAndProjectDir(canonicalConfigPath, discoveryRootCanonical) {
+    const rel = relative(discoveryRootCanonical, canonicalConfigPath);
+    if (rel.split(sep).includes('..'))
+        return;
+    if (!existsSync(canonicalConfigPath))
+        return;
+    rmSync(canonicalConfigPath, { force: true });
+    const parentDir = dirname(canonicalConfigPath);
+    const parentRel = relative(discoveryRootCanonical, parentDir);
+    // Only delete parent when it is a project dir: discoveryRoot/<name>/config.json
+    if (basename(canonicalConfigPath) === 'config.json' &&
+        !parentRel.startsWith('..') &&
+        !parentRel.includes(sep) &&
+        parentRel !== '' &&
+        existsSync(parentDir)) {
+        rmSync(parentDir, { recursive: true, force: true });
+    }
+}
 /**
- * Remove a project from the registry.
- * Does not delete any files.
+ * Remove a project from the registry and delete its config file and project directory
+ * when the config lives under limps/projects (Application Support/limps/projects/).
+ * Accepts either a project name (exact match, no path chars) or a path to a config file.
+ * Paths are strictly validated: must be under limps/projects and end with config.json.
  *
- * @param name - Project name to remove
+ * @param nameOrPath - Project name or path to config.json
  * @returns Success message
- * @throws Error if project not found
+ * @throws Error if project not found or path is invalid
  */
-export function configRemove(name) {
-    unregisterProject(name);
-    return `Removed project "${name}" from registry (files not deleted)`;
+export function configRemove(nameOrPath) {
+    const registry = loadRegistry();
+    const discoveryRoot = getProjectsRoot();
+    let discoveryRootCanonical;
+    try {
+        discoveryRootCanonical = realpathSync(discoveryRoot);
+    }
+    catch {
+        discoveryRootCanonical = discoveryRoot;
+    }
+    if (SAFE_NAME_REGEX.test(nameOrPath)) {
+        if (registry.projects[nameOrPath]) {
+            const configPath = registry.projects[nameOrPath].configPath;
+            let canonicalPath = null;
+            try {
+                canonicalPath = realpathSync(resolve(configPath));
+            }
+            catch {
+                // Config file missing, just unregister
+            }
+            const underDiscovery = canonicalPath !== null &&
+                !relative(discoveryRootCanonical, canonicalPath).split(sep).includes('..');
+            if (underDiscovery && canonicalPath) {
+                deleteConfigAndProjectDir(canonicalPath, discoveryRootCanonical);
+            }
+            unregisterProject(nameOrPath);
+            return underDiscovery
+                ? `Removed project "${nameOrPath}" and deleted config and project directory.`
+                : `Removed project "${nameOrPath}" from registry.`;
+        }
+        throw new Error(`Project not found: ${nameOrPath}\nRun \`limps config list\` to see registered projects.`);
+    }
+    const absolutePath = resolve(nameOrPath);
+    if (basename(absolutePath) !== 'config.json') {
+        throw new Error(`Invalid path: must point to a config.json file.\nRun \`limps config list\` to see registered projects.`);
+    }
+    if (!existsSync(absolutePath)) {
+        throw new Error(`Project not found: ${nameOrPath}\nRun \`limps config list\` to see registered projects.`);
+    }
+    try {
+        const stat = statSync(absolutePath);
+        if (!stat.isFile()) {
+            throw new Error(`Invalid path: not a file.\nRun \`limps config list\` to see registered projects.`);
+        }
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.startsWith('Invalid path:'))
+            throw err;
+        throw new Error(`Project not found: ${nameOrPath}\nRun \`limps config list\` to see registered projects.`);
+    }
+    let canonicalPath;
+    try {
+        canonicalPath = realpathSync(absolutePath);
+    }
+    catch {
+        throw new Error(`Project not found: ${nameOrPath}\nRun \`limps config list\` to see registered projects.`);
+    }
+    const rel = relative(discoveryRootCanonical, canonicalPath);
+    if (rel.split(sep).includes('..')) {
+        throw new Error(`Invalid path: must be under application config directory.\nRun \`limps config list\` to see registered projects.`);
+    }
+    const entry = Object.entries(registry.projects).find(([, p]) => {
+        try {
+            return realpathSync(resolve(p.configPath)) === canonicalPath;
+        }
+        catch {
+            return false;
+        }
+    });
+    if (entry) {
+        const [name] = entry;
+        deleteConfigAndProjectDir(canonicalPath, discoveryRootCanonical);
+        unregisterProject(name);
+        return `Removed project "${name}" and deleted config and project directory.`;
+    }
+    throw new Error(`Project not found: ${nameOrPath}\nRun \`limps config list\` to see registered projects.`);
 }
 /**
  * Set the current project from an existing config file path.
@@ -303,16 +435,15 @@ export function configSet(configFilePath) {
 }
 import { getAdapter, LocalMcpAdapter, } from './mcp-client-adapter.js';
 /**
- * Discover and register config files from default OS locations.
- * Scans the OS-specific application support directories for config.json files.
+ * Discover config files under limps/projects (Application Support/limps/projects/<name>/config.json).
+ * Does not auto-register; use `limps config use <name>` to register and switch.
  *
- * @returns Summary of discovered projects
+ * @returns Summary of discovered (unregistered) projects
  */
 export function configDiscover() {
-    // Get the parent directory of where limps stores its config
+    // Scan under limps/projects (Application Support/limps/projects/<name>/config.json)
     // This respects any mocking of getOSBasePath for testing
-    const limpsBasePath = getOSBasePath('limps');
-    const searchDir = dirname(limpsBasePath);
+    const searchDir = getProjectsRoot();
     const registry = loadRegistry();
     const registeredPaths = new Set(Object.values(registry.projects).map((p) => p.configPath));
     const discovered = [];
@@ -324,18 +455,19 @@ export function configDiscover() {
         for (const entry of entries) {
             if (!entry.isDirectory())
                 continue;
-            const configPath = `${searchDir}/${entry.name}/config.json`;
+            const configPath = join(searchDir, entry.name, 'config.json');
             // Skip if already registered or doesn't exist
             if (registeredPaths.has(configPath) || !existsSync(configPath))
                 continue;
-            // Validate it's a valid limps config
+            // Only list configs that are actually limps configs (plansPath, dataPath, scoring)
             try {
-                loadConfig(configPath);
-                registerProject(entry.name, configPath);
+                const raw = JSON.parse(readFileSync(configPath, 'utf-8'));
+                if (!validateConfig(raw))
+                    continue;
                 discovered.push({ name: entry.name, path: configPath });
             }
             catch {
-                // Not a valid limps config, skip
+                // Not valid JSON or not a limps config, skip
             }
         }
     }
@@ -350,7 +482,250 @@ export function configDiscover() {
         lines.push(`  ${name}: ${path}`);
     }
     lines.push('');
-    lines.push('Run `limps config use <name>` to switch to a project.');
+    lines.push('Run `limps config use <name>` to register and switch to a project.');
+    return lines.join('\n');
+}
+/**
+ * Repair MCP client config references: replace old config path with new path in all
+ * global MCP client configs (Claude Desktop, Cursor, Claude Code, Codex).
+ */
+function repairMcpConfigReferences(oldPath, newPath) {
+    const oldResolved = resolve(oldPath);
+    const newResolved = resolve(newPath);
+    const adapters = ['claude', 'cursor', 'claude-code', 'codex'];
+    for (const clientType of adapters) {
+        try {
+            const adapter = getAdapter(clientType);
+            const config = adapter.readConfig();
+            const serversKey = adapter.getServersKey();
+            let servers;
+            if (adapter.useFlatKey?.()) {
+                servers = config[serversKey];
+            }
+            else {
+                const keyParts = serversKey.split('.');
+                let current = config;
+                for (let i = 0; i < keyParts.length - 1; i++) {
+                    const part = keyParts[i];
+                    if (!current[part] || typeof current[part] !== 'object')
+                        break;
+                    current = current[part];
+                }
+                servers = current[keyParts[keyParts.length - 1]];
+            }
+            if (!servers || typeof servers !== 'object')
+                continue;
+            let changed = false;
+            for (const server of Object.values(servers)) {
+                if (!server ||
+                    typeof server !== 'object' ||
+                    !Array.isArray(server.args))
+                    continue;
+                const args = server.args;
+                for (let i = 0; i < args.length; i++) {
+                    const arg = args[i];
+                    if (typeof arg !== 'string')
+                        continue;
+                    if (arg === oldPath || resolve(arg) === oldResolved) {
+                        args[i] = newResolved;
+                        changed = true;
+                    }
+                }
+            }
+            if (changed)
+                adapter.writeConfig(config);
+        }
+        catch {
+            // Skip if config missing or invalid
+        }
+    }
+}
+/**
+ * Repair all path fields in a config JSON so paths under oldDir are rewritten under targetDir.
+ * Handles plansPath, dataPath, docsPaths (array). Preserves relative structure under the project dir.
+ */
+function repairConfigPaths(raw, oldDir, targetDir) {
+    const oldDirResolved = resolve(oldDir);
+    const targetDirResolved = resolve(targetDir);
+    function rewritePath(pathStr) {
+        const resolved = resolve(pathStr);
+        if (resolved === oldDirResolved || resolved.startsWith(oldDirResolved + sep)) {
+            const rel = relative(oldDirResolved, resolved);
+            return rel === '' ? targetDirResolved : join(targetDirResolved, rel);
+        }
+        return pathStr;
+    }
+    if (raw.plansPath && typeof raw.plansPath === 'string') {
+        raw.plansPath = rewritePath(raw.plansPath);
+    }
+    if (raw.dataPath && typeof raw.dataPath === 'string') {
+        raw.dataPath = rewritePath(raw.dataPath);
+    }
+    if (raw.docsPaths && Array.isArray(raw.docsPaths)) {
+        raw.docsPaths = raw.docsPaths.map((p) => (typeof p === 'string' ? rewritePath(p) : p));
+    }
+}
+/** Write migration log so the run can be reversed. */
+function writeMigrationLog(limpsRoot, moves) {
+    const timestamp = new Date().toISOString();
+    const safeTimestamp = timestamp.replace(/[:.]/g, '-');
+    const logPath = join(limpsRoot, `migration-${safeTimestamp}.json`);
+    const reverseSteps = moves.map((m) => `  ${m.name}: copy "${m.targetPath}" → "${m.sourcePath}", then \`limps config set "${m.sourcePath}"\`, then remove "${m.targetPath}" and its directory.`);
+    const log = {
+        timestamp,
+        command: 'limps config migrate',
+        moves,
+        reverseInstructions: [
+            'To reverse this migration, for each move:',
+            ...reverseSteps,
+            'Then run `limps config remove <name>` for each project and re-add with the source path if desired.',
+        ].join('\n'),
+    };
+    writeFileSync(logPath, JSON.stringify(log, null, 2));
+    return logPath;
+}
+export function configMigrate() {
+    const projectsRoot = getProjectsRoot();
+    const limpsRoot = getOSBasePath('limps');
+    const parentOfLimps = dirname(limpsRoot);
+    mkdirSync(projectsRoot, { recursive: true });
+    const registry = loadRegistry();
+    const lines = ['Migrating configs into limps/projects/', ''];
+    const moves = [];
+    let migrated = 0;
+    function copyConfigToProjectDir(name, sourcePath) {
+        const targetDir = join(projectsRoot, name);
+        const targetPath = join(targetDir, 'config.json');
+        if (!existsSync(sourcePath))
+            return false;
+        try {
+            const raw = JSON.parse(readFileSync(sourcePath, 'utf-8'));
+            if (!validateConfig(raw))
+                return false;
+            const oldDir = dirname(sourcePath);
+            repairConfigPaths(raw, oldDir, targetDir);
+            mkdirSync(targetDir, { recursive: true });
+            writeFileSync(targetPath, JSON.stringify(raw, null, 2));
+            registerProject(name, targetPath);
+            repairMcpConfigReferences(sourcePath, targetPath);
+            rmSync(sourcePath, { force: true });
+            if (basename(sourcePath) === 'config.json' && existsSync(oldDir)) {
+                rmSync(oldDir, { recursive: true, force: true });
+            }
+            migrated++;
+            moves.push({ name, sourcePath, targetPath });
+            lines.push(`  ${name}: ${sourcePath} → ${targetPath}`);
+            return true;
+        }
+        catch {
+            return false;
+        }
+    }
+    // 1. Registered projects not already under limps/projects/<name>/
+    for (const [name, project] of Object.entries(registry.projects)) {
+        const currentPath = resolve(project.configPath);
+        const targetPath = join(projectsRoot, name, 'config.json');
+        let currentCanonical;
+        let targetCanonical;
+        try {
+            currentCanonical = realpathSync(currentPath);
+            targetCanonical = existsSync(targetPath) ? realpathSync(targetPath) : targetPath;
+        }
+        catch {
+            continue;
+        }
+        if (currentCanonical === targetCanonical)
+            continue;
+        const rel = relative(projectsRoot, currentPath);
+        if (!rel.split(sep).includes('..'))
+            continue; // already under projects
+        copyConfigToProjectDir(name, currentPath);
+    }
+    // 2. Old sibling layout: Application Support/<name>/config.json
+    try {
+        if (existsSync(parentOfLimps)) {
+            const entries = readdirSync(parentOfLimps, { withFileTypes: true });
+            for (const entry of entries) {
+                if (!entry.isDirectory() || entry.name === 'limps')
+                    continue;
+                const sourcePath = join(parentOfLimps, entry.name, 'config.json');
+                if (!existsSync(sourcePath))
+                    continue;
+                if (registry.projects[entry.name])
+                    continue; // already registered and possibly migrated
+                copyConfigToProjectDir(entry.name, sourcePath);
+            }
+        }
+    }
+    catch {
+        // ignore
+    }
+    // 3. Flat limps layout: limps/<name>/config.json (excluding projects)
+    try {
+        if (existsSync(limpsRoot)) {
+            const entries = readdirSync(limpsRoot, { withFileTypes: true });
+            for (const entry of entries) {
+                if (!entry.isDirectory() || entry.name === PROJECTS_DIR)
+                    continue;
+                const sourcePath = join(limpsRoot, entry.name, 'config.json');
+                if (!existsSync(sourcePath))
+                    continue;
+                const targetPath = join(projectsRoot, entry.name, 'config.json');
+                if (existsSync(targetPath))
+                    continue; // already in projects
+                copyConfigToProjectDir(entry.name, sourcePath);
+            }
+        }
+    }
+    catch {
+        // ignore
+    }
+    // 4. Strip coordination keys from all project configs under limps/projects/
+    const deprecatedCoordinationKeys = [
+        'coordinationPath',
+        'heartbeatTimeout',
+        'debounceDelay',
+        'maxHandoffIterations',
+    ];
+    let coordinationCleaned = 0;
+    try {
+        const projectDirs = readdirSync(projectsRoot, { withFileTypes: true });
+        for (const entry of projectDirs) {
+            if (!entry.isDirectory())
+                continue;
+            const configPath = join(projectsRoot, entry.name, 'config.json');
+            if (!existsSync(configPath))
+                continue;
+            try {
+                const raw = readFileSync(configPath, 'utf-8');
+                const hadDeprecated = deprecatedCoordinationKeys.some((k) => raw.includes(`"${k}"`));
+                if (hadDeprecated) {
+                    loadConfig(configPath);
+                    coordinationCleaned++;
+                }
+            }
+            catch {
+                // ignore
+            }
+        }
+    }
+    catch {
+        // ignore
+    }
+    if (coordinationCleaned > 0) {
+        lines.push('');
+        lines.push(`Coordination keys removed from ${coordinationCleaned} config(s).`);
+    }
+    if (migrated === 0) {
+        if (coordinationCleaned === 0) {
+            return 'No configs to migrate. All known configs are already under limps/projects/.';
+        }
+        return lines.join('\n');
+    }
+    const logPath = writeMigrationLog(limpsRoot, moves);
+    lines.push('');
+    lines.push(`Migrated ${migrated} project(s). Run \`limps config list\` to see current projects.`);
+    lines.push(`Reversal log: ${logPath}`);
     return lines.join('\n');
 }
 /**