@orderful/droid 0.27.2 → 0.27.4

package/CHANGELOG.md

@@ -1,5 +1,42 @@
 # @orderful/droid
 
+## 0.27.4
+
+### Patch Changes
+
+- [`c5bd82e`](https://github.com/Orderful/droid/commit/c5bd82e96202bd13fa71e57e45b5b2039ad95e6b) Thanks [@frytyler](https://github.com/frytyler)! - Add filesystem sync migration to fix untracked installations
+
+  **New migration (v0.27.4):**
+
+  Scans installed skills on the filesystem and adds any that aren't tracked in config. This is a one-time cleanup to fix inconsistencies from the v0.27.x migration series.
+
+  **What it does:**
+  - Scans `~/.claude/skills/` and `~/.config/opencode/skills/`
+  - Identifies installed skills missing from config
+  - Adds them with correct versions from bundled tool manifests
+  - Only processes known droid tool skills (ignores custom directories)
+
+  **Impact:**
+
+  Tools that were physically installed but not tracked (like `brain` and `comments`) will now show as properly installed with checkmarks in the TUI.
+
+## 0.27.3
+
+### Patch Changes
+
+- [#152](https://github.com/Orderful/droid/pull/152) [`8bd3a4f`](https://github.com/Orderful/droid/commit/8bd3a4f4c6ef1352ed683be584693124a202f35a) Thanks [@frytyler](https://github.com/frytyler)! - Fix config skill name migration actually persisting changes to disk
+
+  **Bug fixes:**
+  - **Per-platform change tracking**: Migration now uses a `platformChanged` flag to track changes independently for each platform, ensuring all platform configs are properly saved
+  - **Prevent config overwrites**: `runPackageMigrations` now reloads config before saving the version marker, preventing stale data from overwriting migration changes
+  - **Remove conflicting legacy code**: Deleted v0.18.0 migration fallback that was actively undoing the config renaming by deleting newly-migrated unprefixed entries
+
+  **Impact:**
+
+  The v0.27.2 config migration now successfully renames tool entries (e.g. `droid-codex` → `codex`) and persists changes to `~/.droid/config.yaml`. Tools will correctly show as installed in the TUI after upgrade.
+
+  This completes the fix for tools showing as "not installed" after upgrading to v0.27.x.
+
 ## 0.27.2
 
 ### Patch Changes

package/dist/bin/droid.js

@@ -352,16 +352,6 @@ function getInstalledToolVersion(toolName) {
     if (installedTools[skillName]) {
       return installedTools[skillName].version;
     }
-    if (skillName.startsWith("droid-")) {
-      const oldSkillName = skillName.replace(/^droid-/, "");
-      if (installedTools[oldSkillName]) {
-        const version2 = installedTools[oldSkillName].version;
-        delete installedTools[oldSkillName];
-        setPlatformTools(config, installedTools);
-        saveConfig(config);
-        return version2;
-      }
-    }
   }
   return null;
 }
@@ -628,6 +618,7 @@ function createConfigSkillNameMigration(version2) {
         config.platform = platformKey;
         const trackedTools = getPlatformTools(config);
         const skillNames = Object.keys(trackedTools);
+        let platformChanged = false;
         for (const skillName of skillNames) {
           if (!skillName.startsWith("droid-") || skillName === "droid") {
             continue;
@@ -636,10 +627,61 @@ function createConfigSkillNameMigration(version2) {
           if (!trackedTools[unprefixedName]) {
             trackedTools[unprefixedName] = trackedTools[skillName];
             delete trackedTools[skillName];
+            platformChanged = true;
             configChanged = true;
           }
         }
-        if (configChanged) {
+        if (platformChanged) {
+          setPlatformTools(config, trackedTools);
+        }
+      }
+      config.platform = originalPlatform;
+      if (configChanged) {
+        saveConfig(config);
+      }
+    }
+  };
+}
+function createFilesystemSyncMigration(version2) {
+  return {
+    version: version2,
+    description: "Sync config with actually installed skills on filesystem",
+    up: () => {
+      const config = loadConfig();
+      const originalPlatform = config.platform;
+      let configChanged = false;
+      for (const platformKey of ["claude-code" /* ClaudeCode */, "opencode" /* OpenCode */]) {
+        if (!config.platforms[platformKey]) continue;
+        const skillsPath = getSkillsPath(platformKey);
+        if (!existsSync4(skillsPath)) continue;
+        config.platform = platformKey;
+        const trackedTools = getPlatformTools(config);
+        let platformChanged = false;
+        const bundledTools = getBundledTools();
+        const allToolNames = new Set(
+          bundledTools.flatMap(
+            (tool) => tool.includes.skills.map((s) => s.name)
+          )
+        );
+        const installedDirs = readdirSync3(skillsPath, { withFileTypes: true }).filter((dirent) => dirent.isDirectory()).map((dirent) => dirent.name);
+        for (const dirName of installedDirs) {
+          if (!allToolNames.has(dirName)) continue;
+          if (trackedTools[dirName]) continue;
+          let version3 = "0.0.0";
+          const matchingTool = bundledTools.find(
+            (tool) => tool.includes.skills.some((s) => s.name === dirName && s.required)
+          );
+          if (matchingTool) {
+            version3 = matchingTool.version;
+          }
+          trackedTools[dirName] = {
+            version: version3,
+            installed_at: (/* @__PURE__ */ new Date()).toISOString()
+          };
+          platformChanged = true;
+          configChanged = true;
+        }
+        if (platformChanged) {
           setPlatformTools(config, trackedTools);
         }
       }
@@ -652,7 +694,8 @@ function createConfigSkillNameMigration(version2) {
 }
 var PACKAGE_MIGRATIONS = [
   createPlatformSyncMigration("0.25.0"),
-  createConfigSkillNameMigration("0.27.2")
+  createConfigSkillNameMigration("0.27.2"),
+  createFilesystemSyncMigration("0.27.4")
 ];
 var TOOL_MIGRATIONS = {
   brain: [createConfigDirMigration("droid-brain", "0.2.3")],
@@ -740,9 +783,10 @@ function runPackageMigrations(packageVersion) {
     return afterFrom && beforeOrAtTo;
   });
   if (pendingMigrations.length === 0) {
-    config.migrations = config.migrations || {};
-    config.migrations.package = packageVersion;
-    saveConfig(config);
+    const freshConfig = loadConfig();
+    freshConfig.migrations = freshConfig.migrations || {};
+    freshConfig.migrations.package = packageVersion;
+    saveConfig(freshConfig);
     return { success: true };
   }
   const configDir = getConfigDir();
@@ -765,9 +809,10 @@ function runPackageMigrations(packageVersion) {
       };
     }
   }
-  config.migrations = config.migrations || {};
-  config.migrations.package = packageVersion;
-  saveConfig(config);
+  const updatedConfig = loadConfig();
+  updatedConfig.migrations = updatedConfig.migrations || {};
+  updatedConfig.migrations.package = packageVersion;
+  saveConfig(updatedConfig);
   return { success: true };
 }
 

package/dist/index.js

@@ -591,6 +591,7 @@ function createConfigSkillNameMigration(version) {
         config.platform = platformKey;
         const trackedTools = getPlatformTools(config);
         const skillNames = Object.keys(trackedTools);
+        let platformChanged = false;
         for (const skillName of skillNames) {
           if (!skillName.startsWith("droid-") || skillName === "droid") {
             continue;
@@ -599,10 +600,61 @@ function createConfigSkillNameMigration(version) {
           if (!trackedTools[unprefixedName]) {
             trackedTools[unprefixedName] = trackedTools[skillName];
             delete trackedTools[skillName];
+            platformChanged = true;
             configChanged = true;
           }
         }
-        if (configChanged) {
+        if (platformChanged) {
+          setPlatformTools(config, trackedTools);
+        }
+      }
+      config.platform = originalPlatform;
+      if (configChanged) {
+        saveConfig(config);
+      }
+    }
+  };
+}
+function createFilesystemSyncMigration(version) {
+  return {
+    version,
+    description: "Sync config with actually installed skills on filesystem",
+    up: () => {
+      const config = loadConfig();
+      const originalPlatform = config.platform;
+      let configChanged = false;
+      for (const platformKey of ["claude-code" /* ClaudeCode */, "opencode" /* OpenCode */]) {
+        if (!config.platforms[platformKey]) continue;
+        const skillsPath = getSkillsPath(platformKey);
+        if (!existsSync4(skillsPath)) continue;
+        config.platform = platformKey;
+        const trackedTools = getPlatformTools(config);
+        let platformChanged = false;
+        const bundledTools = getBundledTools();
+        const allToolNames = new Set(
+          bundledTools.flatMap(
+            (tool) => tool.includes.skills.map((s) => s.name)
+          )
+        );
+        const installedDirs = readdirSync3(skillsPath, { withFileTypes: true }).filter((dirent) => dirent.isDirectory()).map((dirent) => dirent.name);
+        for (const dirName of installedDirs) {
+          if (!allToolNames.has(dirName)) continue;
+          if (trackedTools[dirName]) continue;
+          let version2 = "0.0.0";
+          const matchingTool = bundledTools.find(
+            (tool) => tool.includes.skills.some((s) => s.name === dirName && s.required)
+          );
+          if (matchingTool) {
+            version2 = matchingTool.version;
+          }
+          trackedTools[dirName] = {
+            version: version2,
+            installed_at: (/* @__PURE__ */ new Date()).toISOString()
+          };
+          platformChanged = true;
+          configChanged = true;
+        }
+        if (platformChanged) {
           setPlatformTools(config, trackedTools);
         }
       }
@@ -615,7 +667,8 @@ function createConfigSkillNameMigration(version) {
 }
 var PACKAGE_MIGRATIONS = [
   createPlatformSyncMigration("0.25.0"),
-  createConfigSkillNameMigration("0.27.2")
+  createConfigSkillNameMigration("0.27.2"),
+  createFilesystemSyncMigration("0.27.4")
 ];
 var TOOL_MIGRATIONS = {
   brain: [createConfigDirMigration("droid-brain", "0.2.3")],

package/dist/lib/config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../../src/lib/config.ts"],"names":[],"mappings":"AAIA,OAAO,EAGL,KAAK,WAAW,EAEhB,KAAK,cAAc,EACnB,KAAK,gBAAgB,EACtB,MAAM,SAAS,CAAC;AAmDjB;;GAEG;AACH,wBAAgB,eAAe,IAAI,IAAI,CAItC;AAED;;GAEG;AACH,wBAAgB,YAAY,IAAI,OAAO,CAEtC;AAED;;;GAGG;AACH,wBAAgB,UAAU,IAAI,WAAW,CA4BxC;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,MAAM,EAAE,WAAW,GAAG,IAAI,CAKpD;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAanD;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,GAAG,IAAI,CAiBhE;AAED;;GAEG;AACH,wBAAgB,aAAa,IAAI,MAAM,CAEtC;AAED;;GAEG;AACH,wBAAgB,YAAY,IAAI,MAAM,CAErC;AAWD;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAG/D;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,SAAS,EAAE,MAAM,GAAG,cAAc,CAapE;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAChC,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,cAAc,GACxB,IAAI,CAWN;AAED;;GAEG;AACH,wBAAgB,mBAAmB,IAAI,gBAAgB,CAMtD;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAQ5E"}

package/dist/lib/migrations.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../src/lib/migrations.ts"],"names":[],"mappings":"AAUA,OAAO,EACL,KAAK,SAAS,EAIf,MAAM,SAAS,CAAC;AAiOjB;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAAE,CAE/D;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAc/D;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,MAAM,GACd,IAAI,CAmBN;AAED;;;GAGG;AACH,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CA2CtC;AAED;;;GAGG;AACH,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,MAAM,EAChB,gBAAgB,EAAE,MAAM,GACvB;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAStC;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,cAAc,EAAE,MAAM,GAAG;IAC5D,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB,CAqDA"}
+{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../src/lib/migrations.ts"],"names":[],"mappings":"AAUA,OAAO,EACL,KAAK,SAAS,EAIf,MAAM,SAAS,CAAC;AA8SjB;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAAE,CAE/D;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAc/D;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,MAAM,GACd,IAAI,CAmBN;AAED;;;GAGG;AACH,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CA2CtC;AAED;;;GAGG;AACH,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,MAAM,EAChB,gBAAgB,EAAE,MAAM,GACvB;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAStC;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,cAAc,EAAE,MAAM,GAAG;IAC5D,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB,CAyDA"}

package/dist/lib/tools.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"tools.d.ts","sourceRoot":"","sources":["../../src/lib/tools.ts"],"names":[],"mappings":"AAKA,OAAO,EACL,KAAK,YAAY,EAIlB,MAAM,SAAS,CAAC;AAMjB;;GAEG;AACH,wBAAgB,kBAAkB,IAAI,MAAM,CAE3C;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,YAAY,GAAG,IAAI,CAyBrE;AAED;;GAEG;AACH,wBAAgB,eAAe,IAAI,YAAY,EAAE,CAmBhD;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAczD;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAiCvE;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,OAAO,CAAC;IACnB,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,cAAc,CAuBpE;AAED;;GAEG;AACH,wBAAgB,mBAAmB,IAAI,cAAc,EAAE,CA2BtD"}
+{"version":3,"file":"tools.d.ts","sourceRoot":"","sources":["../../src/lib/tools.ts"],"names":[],"mappings":"AAKA,OAAO,EACL,KAAK,YAAY,EAGlB,MAAM,SAAS,CAAC;AAMjB;;GAEG;AACH,wBAAgB,kBAAkB,IAAI,MAAM,CAE3C;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,YAAY,GAAG,IAAI,CAyBrE;AAED;;GAEG;AACH,wBAAgB,eAAe,IAAI,YAAY,EAAE,CAmBhD;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAczD;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAmBvE;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,OAAO,CAAC;IACnB,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,cAAc,CAuBpE;AAED;;GAEG;AACH,wBAAgB,mBAAmB,IAAI,cAAc,EAAE,CA2BtD"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@orderful/droid",
-  "version": "0.27.2",
+  "version": "0.27.4",
   "description": "AI workflow toolkit for sharing skills, commands, and agents across the team",
   "type": "module",
   "bin": {

package/src/lib/config.ts

@@ -2,14 +2,21 @@ import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'fs';
 import { homedir } from 'os';
 import { join } from 'path';
 import YAML from 'yaml';
-import { Platform, BuiltInOutput, type DroidConfig, type LegacyDroidConfig, type SkillOverrides, type AutoUpdateConfig } from './types';
+import {
+  Platform,
+  BuiltInOutput,
+  type DroidConfig,
+  type LegacyDroidConfig,
+  type SkillOverrides,
+  type AutoUpdateConfig,
+} from './types';
 
 const CONFIG_DIR = join(homedir(), '.droid');
 const CONFIG_FILE = join(CONFIG_DIR, 'config.yaml');
 
 const DEFAULT_AUTO_UPDATE: AutoUpdateConfig = {
-  app: false,   // Opt-in: user must enable
-  tools: true,  // Opt-out: enabled by default (tools only update when app updates)
+  app: false, // Opt-in: user must enable
+  tools: true, // Opt-out: enabled by default (tools only update when app updates)
 };
 
 const DEFAULT_CONFIG: DroidConfig = {
@@ -25,14 +32,17 @@ const DEFAULT_CONFIG: DroidConfig = {
  * v1: ai_tool + skills flat
  * v2: platform + platforms map with per-platform tools
  */
-function migrateConfig(config: Partial<DroidConfig> & Partial<LegacyDroidConfig>): DroidConfig {
+function migrateConfig(
+  config: Partial<DroidConfig> & Partial<LegacyDroidConfig>,
+): DroidConfig {
   // Check if this is a legacy config (has ai_tool, no platform)
   if ('ai_tool' in config && !('platform' in config)) {
     const legacyConfig = config as LegacyDroidConfig;
     return {
       platform: legacyConfig.ai_tool,
       user_mention: legacyConfig.user_mention ?? DEFAULT_CONFIG.user_mention,
-      output_preference: legacyConfig.output_preference ?? DEFAULT_CONFIG.output_preference,
+      output_preference:
+        legacyConfig.output_preference ?? DEFAULT_CONFIG.output_preference,
       git_username: legacyConfig.git_username ?? DEFAULT_CONFIG.git_username,
       platforms: {
         [legacyConfig.ai_tool]: {
@@ -79,7 +89,8 @@ export function loadConfig(): DroidConfig {
 
   try {
     const content = readFileSync(CONFIG_FILE, 'utf-8');
-    const rawConfig = YAML.parse(content) as Partial<DroidConfig> & Partial<LegacyDroidConfig>;
+    const rawConfig = YAML.parse(content) as Partial<DroidConfig> &
+      Partial<LegacyDroidConfig>;
 
     // Check if migration is needed
     // TODO: Remove after v0.14.0 (target: late Jan 2025)
@@ -133,7 +144,10 @@ export function getConfigValue(key: string): unknown {
 export function setConfigValue(key: string, value: unknown): void {
   const config = loadConfig();
   const keys = key.split('.');
-  let current: Record<string, unknown> = config as unknown as Record<string, unknown>;
+  let current: Record<string, unknown> = config as unknown as Record<
+    string,
+    unknown
+  >;
 
   for (let i = 0; i < keys.length - 1; i++) {
     if (current[keys[i]] === undefined) {
@@ -198,7 +212,10 @@ export function loadSkillOverrides(skillName: string): SkillOverrides {
 /**
  * Save skill-specific overrides
  */
-export function saveSkillOverrides(skillName: string, overrides: SkillOverrides): void {
+export function saveSkillOverrides(
+  skillName: string,
+  overrides: SkillOverrides,
+): void {
   const normalizedName = normalizeSkillNameForConfig(skillName);
   const overridesPath = getSkillOverridesPath(skillName);
   const skillDir = join(CONFIG_DIR, 'skills', normalizedName);

package/src/lib/migrations.ts

@@ -179,6 +179,7 @@ function createConfigSkillNameMigration(version: string): Migration {
         config.platform = platformKey;
         const trackedTools = getPlatformTools(config);
         const skillNames = Object.keys(trackedTools);
+        let platformChanged = false;
 
         for (const skillName of skillNames) {
           // Skip if already unprefixed or is the special 'droid' tool
@@ -192,11 +193,86 @@ function createConfigSkillNameMigration(version: string): Migration {
           if (!trackedTools[unprefixedName]) {
             trackedTools[unprefixedName] = trackedTools[skillName];
             delete trackedTools[skillName];
+            platformChanged = true;
             configChanged = true;
           }
         }
 
-        if (configChanged) {
+        if (platformChanged) {
+          setPlatformTools(config, trackedTools);
+        }
+      }
+
+      config.platform = originalPlatform;
+      if (configChanged) {
+        saveConfig(config);
+      }
+    },
+  };
+}
+
+/**
+ * Sync config with filesystem - add any installed skills that aren't tracked
+ * This is a one-time cleanup migration to fix config inconsistencies from v0.27.x
+ */
+function createFilesystemSyncMigration(version: string): Migration {
+  return {
+    version,
+    description: 'Sync config with actually installed skills on filesystem',
+    up: () => {
+      const config = loadConfig();
+      const originalPlatform = config.platform;
+      let configChanged = false;
+
+      // Check both platforms
+      for (const platformKey of [Platform.ClaudeCode, Platform.OpenCode]) {
+        if (!config.platforms[platformKey]) continue;
+
+        const skillsPath = getSkillsPath(platformKey);
+        if (!existsSync(skillsPath)) continue;
+
+        config.platform = platformKey;
+        const trackedTools = getPlatformTools(config);
+        let platformChanged = false;
+
+        // Get all tool names from manifests
+        const bundledTools = getBundledTools();
+        const allToolNames = new Set(
+          bundledTools.flatMap((tool) =>
+            tool.includes.skills.map((s) => s.name),
+          ),
+        );
+
+        // Scan filesystem for installed skills
+        const installedDirs = readdirSync(skillsPath, { withFileTypes: true })
+          .filter((dirent) => dirent.isDirectory())
+          .map((dirent) => dirent.name);
+
+        for (const dirName of installedDirs) {
+          // Skip if not a known tool skill
+          if (!allToolNames.has(dirName)) continue;
+
+          // Skip if already tracked
+          if (trackedTools[dirName]) continue;
+
+          // Try to get version from bundled tool
+          let version = '0.0.0';
+          const matchingTool = bundledTools.find((tool) =>
+            tool.includes.skills.some((s) => s.name === dirName && s.required),
+          );
+          if (matchingTool) {
+            version = matchingTool.version;
+          }
+
+          trackedTools[dirName] = {
+            version,
+            installed_at: new Date().toISOString(),
+          };
+          platformChanged = true;
+          configChanged = true;
+        }
+
+        if (platformChanged) {
           setPlatformTools(config, trackedTools);
         }
       }
@@ -218,6 +294,7 @@ function createConfigSkillNameMigration(version: string): Migration {
 const PACKAGE_MIGRATIONS: Migration[] = [
   createPlatformSyncMigration('0.25.0'),
   createConfigSkillNameMigration('0.27.2'),
+  createFilesystemSyncMigration('0.27.4'),
 ];
 
 /**
@@ -387,9 +464,11 @@ export function runPackageMigrations(packageVersion: string): {
 
   if (pendingMigrations.length === 0) {
     // No migrations to run, but still update the version marker
-    config.migrations = config.migrations || {};
-    config.migrations.package = packageVersion;
-    saveConfig(config);
+    // Reload config in case it was modified elsewhere
+    const freshConfig = loadConfig();
+    freshConfig.migrations = freshConfig.migrations || {};
+    freshConfig.migrations.package = packageVersion;
+    saveConfig(freshConfig);
     return { success: true };
   }
 
@@ -418,8 +497,10 @@ export function runPackageMigrations(packageVersion: string): {
   }
 
   // All migrations succeeded, update version marker
-  config.migrations = config.migrations || {};
-  config.migrations.package = packageVersion;
-  saveConfig(config);
+  // Reload config in case migrations modified it
+  const updatedConfig = loadConfig();
+  updatedConfig.migrations = updatedConfig.migrations || {};
+  updatedConfig.migrations.package = packageVersion;
+  saveConfig(updatedConfig);
   return { success: true };
 }

package/src/lib/tools.ts

@@ -2,12 +2,11 @@ import { existsSync, readdirSync, readFileSync } from 'fs';
 import { join, dirname } from 'path';
 import { fileURLToPath } from 'url';
 import YAML from 'yaml';
-import { loadConfig, saveConfig } from './config';
+import { loadConfig } from './config';
 import {
   type ToolManifest,
   type ToolIncludes,
   getPlatformTools,
-  setPlatformTools,
 } from './types';
 import { compareSemver } from './version';
 
@@ -113,20 +112,6 @@ export function getInstalledToolVersion(toolName: string): string | null {
     if (installedTools[skillName]) {
       return installedTools[skillName].version;
     }
-
-    // Migration fallback (v0.18.0): Check for old skill name without droid- prefix
-    // This allows tools to show as "update available" rather than "not installed"
-    if (skillName.startsWith('droid-')) {
-      const oldSkillName = skillName.replace(/^droid-/, '');
-      if (installedTools[oldSkillName]) {
-        const version = installedTools[oldSkillName].version;
-        // Clean up stale config entry now that we've detected it
-        delete installedTools[oldSkillName];
-        setPlatformTools(config, installedTools);
-        saveConfig(config);
-        return version;
-      }
-    }
   }
 
   return null;