Switch to git dependencies and add .1aln documentation

Now using git dependencies for onecode-rs and fastga-rs with all fixes:
- onecode-rs: d0b29fd8 (GDB skeleton reading fix)
- fastga-rs: 366f6019 (PATH setup and schema fixes)

Added comprehensive documentation of the GDB skeleton bug and contig→scaffold
mapping fix in GDB_SKELETON_READING_BUG.md.

All tests passing with git dependencies. .1aln filtering now fully functional.

Author: ekg