Fix incremental query bug and improve marker handling

[maynardflies]

Summary

This PR fixes critical bugs in incremental query mode and significantly expands test coverage for the 0.0.3 release.

Changes

Bug Fixes

• Fix incremental query overwrite bug - Results now correctly append to existing files instead of overwriting them
• Fix CETUS_DATA_DIR env var not being respected - Marker storage now properly respects the environment variable
• Fix flaky E2E test - Added --no-marker to nonexistent directory test to ensure consistent behavior

New E2E Tests (122 total tests)

Added comprehensive test coverage including:

• Alert results output formats - CSV and JSONL export to file
• Streaming on alerting index - Stdout and file output modes
• Config file corruption handling - Malformed TOML and empty file recovery
• Alerts list to file - CSV and JSONL export
• Output prefix with --no-marker - Combined flag behavior
• Backtest with streaming and output prefix - Complex workflow testing

Improvements

• Separate marker modes - Clearer separation between direct mode (stdout, no markers) and collector mode (file output with markers)
• README updates - Documentation for the new operating modes

CI/CD

• Run tests on all branch pushes - CI now provides feedback on feature branches before merging
• Skip slow tests - --media all tests marked as skip to prevent CI timeouts

Housekeeping

• Add tmpclaude-* to gitignore
• Remove temp files
• Fix E2E test for prefix mode (add --format jsonl)

Testing

• All unit tests pass (319 passed)
• All E2E tests pass (118 passed, 3 skipped)
• Manual testing of CLI functionality ahead of 0.0.3 release

Test Categories (122 total)

Category	Tests
Query endpoints	4
Streaming	2
Alerts API	2
Async methods	2
CLI commands	4
File output modes	4
Incremental queries	2
Markers management	5
Error handling	4
Edge cases	6
Alert operations	8
Config validation	4
Output formats	8
And more...	67

Breaking Changes

None - existing CLI usage remains compatible.