test(core): add comprehensive coverage tests for CustomToolRegistry

Add 33 new tests targeting previously uncovered paths in custom-tool-registry.ts:
- loadFromDirectory error handling (empty dirs, mixed files, .js support)
- loadFromDirectoryIfStale behavior (non-existent dirs, staleness detection)
- loadFromDirectories / loadFromDirectoriesIfStale edge cases
- register with source path option
- clearCache disk cleanup (.mjs removal, subdirectory cleanup)
- copyEnvFiles private method (copying, directory skipping, empty dirs, missing dirs)
- getAllSerialized with parameters schema
- extension path and nodePaths options
- size getter behavior
- validate edge cases (null name, non-string description, bad params)

Author: easonliang28