feat: add env support for controlling indexing of dotfiles

[midweste]

Summary

Add INCLUDE_DOT_FILES environment variable to control whether dot-directories (e.g. .agent, .config) are included during indexing. By default, dot-directories remain excluded to preserve existing behavior.

Changes

• Modified src/services/indexer.ts: read INCLUDE_DOT_FILES env var and pass it to the glob dot option (previously hardcoded to false)
• Updated README.md: added INCLUDE_DOT_FILES to the "Respects ignore rules" feature bullet and to the Indexing Behavior env var table
• Added 4 unit tests in tests/unit/indexer.test.ts covering default exclusion, true inclusion, case-insensitivity, and rejection of non-true values

Type of change

• New feature (non-breaking change that adds functionality)
• Documentation update
• Test coverage improvement

Testing

• Unit tests pass (npm run test:unit)
• Integration tests pass (npm run test:integration) — if applicable
• TypeScript compiles cleanly (npx tsc --noEmit)
• New tests added for new/changed functionality

Checklist

• My code follows the existing code style and conventions
• I have added/updated JSDoc comments where appropriate
• I have updated documentation (README.md / DEVELOPER.md) if needed
• I have read the Contributing Guide
• I agree to the Contributor License Agreement

Related issues

None

[midweste]

May consider making dot files included by default. Since gitignore is already respected it seems anything that is in a dotfile or dotfolder is likely part of the codebase that could benefit from indexing.