fix: security and documentation fixes

- fix(utils.js): prevent command injection in commandExists() by using
  spawnSync instead of execSync with string interpolation, and validate
  input to only allow alphanumeric chars, dash, underscore, dot (#42)

- fix(utils.js): add security documentation to runCommand() warning
  against passing user-controlled input

- fix(setup-package-manager.js): replace <script> and <binary> with
  [script-name] and [binary-name] to avoid XSS scanner false positives (#43)

- fix(doc-updater.md): replace invalid 'npx ts-morph' with correct
  'npx tsx scripts/codemaps/generate.ts' since ts-morph is a library,
  not a CLI tool (#51)

Fixes #42, #43, #51

agents/doc-updater.md

@@ -27,8 +27,8 @@ You are a documentation specialist focused on keeping codemaps and documentation
 
 ### Analysis Commands
 ```bash
-# Analyze TypeScript project structure
-npx ts-morph
+# Analyze TypeScript project structure (run custom script using ts-morph library)
+npx tsx scripts/codemaps/generate.ts
 
 # Generate dependency graph
 npx madge --image graph.svg src/