Fix script path truncation by centralizing relative path computation

The old code computed relative paths by doing string arithmetic with
dropFirst(extensionsPathString.count + 1), but extensionsPathString
came from URL.appendingPathComponent("./commands") which preserved the
literal "./" — making it 2 chars longer than the actual resolved file
paths from FileManager. Every script path was silently truncated
(system/ → stem/, apps/ → ps/, etc.) for all 851 scripts.

Replace both callsites with a new URL.relativePath(from:) helper that
standardizes both sides before computing the relative path, eliminating
the mismatch entirely. extensionsPathString is no longer needed and
is removed.

Also regenerates commands/extensions.json and commands/README.md with
correct paths.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: grzegorzkrukowski

Tools/Toolkit/Sources/ToolkitLibrary/Core/Stores/DataManager.swift

@@ -22,10 +22,6 @@ public actor DataManager {
     data.metadata.isEmpty
   }
 
-  nonisolated var extensionsPathString: String {
-    extensionsPath.path
-  }
-
   public init(extensionsPath path: String, extensionsFilename: String = "") throws {
     let resolvedPath = URL.resolvingPath(path)
 

Tools/Toolkit/Sources/ToolkitLibrary/Core/Toolkit/Toolkit+ReadContent.swift

@@ -78,8 +78,7 @@ extension Toolkit {
           guard let content = readContentFile(from: file), !content.isEmpty else {
             continue
           }
-          let pathCount = dataManager.extensionsPathString.count + 1
-          readmePath = String(file.path.dropFirst(pathCount))
+          readmePath = file.relativePath(from: dataManager.extensionsPath)
         } else if var scriptCommand = await readScriptCommand(from: file) {
           await dataManager.increaseTotal()
           await dataManager.addLanguage(scriptCommand.language)
@@ -147,9 +146,7 @@ extension Toolkit {
     var dictionary = readKeyValues(of: content)
     dictionary[filenameKey] = filename
 
-    let pathCount = dataManager.extensionsPathString.count + 1
-    let parentDir = fileURL.deletingLastPathComponent().path
-    let scriptPath = String(parentDir.dropFirst(pathCount))
+    let scriptPath = fileURL.deletingLastPathComponent().relativePath(from: dataManager.extensionsPath)
     dictionary["path"] = "\(scriptPath)/"
 
     if !dataManager.ignoreGitInformation {

Tools/Toolkit/Sources/ToolkitLibrary/Extensions/URL/URL+FileSystem.swift

@@ -35,6 +35,16 @@ extension URL {
     )
   }
 
+  /// Returns the path of `self` relative to `base`, with both sides standardized
+  /// so that `./`-prefixed or symlinked inputs produce the same result.
+  func relativePath(from base: URL) -> String {
+    let basePath = base.standardized.path
+    let selfPath = standardized.path
+    guard selfPath.hasPrefix(basePath) else { return selfPath }
+    let stripped = selfPath.dropFirst(basePath.count)
+    return String(stripped.hasPrefix("/") ? stripped.dropFirst() : stripped)
+  }
+
   /// Resolves a path string to an absolute URL.
   /// Handles absolute paths, tilde-prefixed paths, and relative-to-cwd paths.
   static func resolvingPath(_ path: String) -> URL {