Critical bug fix and minor fixes

• Fix #65: Check source directories exist before writing to requirements-mxdev.txt. In offline mode: missing sources log WARNING and are written as comments (expected behavior). In non-offline mode: missing sources log ERROR and mxdev exits with RuntimeError (fatal error indicating checkout failure). This fixes mxmake two-stage installation workflow and prevents silent failures when sources fail to check out.
  [jensens]
• Fix: Configuration parsing no longer logs "Can not parse override:" errors when version-overrides is empty. Empty lines in version-overrides and ignores are now properly skipped during parsing. Also fixed bug where ignores lines were not properly stripped of whitespace.
  [jensens]
• Fix: Three tests that were accidentally marked as skipped during PR #66 merge are now fixed and passing: test_resolve_dependencies_simple_file (fixed assertion to check line contents), test_write_output_with_ignores (fixed to use read() for proper ignore processing), and test_write_relative_constraints_path_different_dirs (fixed to include constraints content).
  [jensens]
• Chore: Improved test coverage for main.py from 42% to 100%. Added comprehensive tests for the main() function covering all CLI argument combinations (--verbose, --silent, --offline, --threads, --no-fetch, --fetch-only), ensuring robust testing of the entry point and all code paths.
  [jensens]
• Chore: Updated test fixture data versions to resolve Dependabot security alerts. Updated urllib3 from 1.26.9 to 2.5.0 and requests from 2.28.0 to 2.32.4 in test data files. These are test fixtures only and were never actual dependencies or security risks. Resolves GitHub Dependabot alerts #1-7.
  [jensens]
• Fix: Add 'synchronize' event to pull_request workflow triggers. This ensures CI runs when PRs are updated with new commits (e.g., after rebasing or pushing new changes), not just when opened or reopened.
  [jensens]
• Chore: Optimize GitHub Actions to prevent duplicate workflow runs on pull requests. Restrict push trigger to only run on main branch, so PRs only trigger via pull_request event. This reduces CI resource usage by 50% for PR workflows.
  [jensens]
• Fix: process_line() now correctly comments out packages in override_keys and ignore_keys for both requirements and constraints files. Previously, these settings only applied to constraints files (variety="c"). Now they work for requirements files (variety="r") as well, with the message "-> mxdev disabled (version override)" for override_keys in requirements.
  [jensens]