Fix config/CLI gather merge and consistent output path roots

[joshuacc]

Summary

• Preserve command provenance by tracking which config directory each command came from, plus a default config root.
• Merge CLI files/urls options with command-defined gather values instead of replacing them.
• Add mergeCommandConfigWithCli to centralize merge behavior and source metadata construction.
• Update FilesAgent to support mixed-source file options (config + CLI) while keeping source-specific path resolution.
• Render gathered file names relative to the active config root when one exists; otherwise render relative to current working directory.

Tests

• Added src/config.spec.ts for home/project config precedence and command directory mapping.
• Added src/mergeCommandConfig.spec.ts for merge semantics and source map behavior.
• Extended src/filesAgent.spec.ts for config-root-relative output naming and mixed-source resolution behavior.
• Ran npm run check successfully.