Various fixes, plus install additional apt packages

[ZedThree]

• Replace absolute paths in compile_commands.json if it exists
  • Needed due to container-based Actions being mounted in a different location, and clang-tidy not accepting relative paths
• Add argument to install additional apt packages
  • Needed to bring in headers for third-party dependencies
• Fix for PRs with multiple files
• Fix for whitespace in code-blocks in comments