Docs/code ocean sync flow

[maggiecam]

Summary

Adds automated Code Ocean reverse-sync support so [sync] commits pushed from co/<module> branches can create draft co-sync/* PRs back into the OMIX monorepo.

Changes

• Adds .github/workflows/auto-cosync-pr.yml

  • Triggers on pushes to co/** when the commit message contains [sync]
  • Creates a fresh co-sync/<module>-* branch from main
  • Reverse-syncs the Code Ocean export into modules/<module>/runtime/
  • Aborts if any changed path falls outside the target module runtime
  • Opens a draft PR to main

• Adds .github/workflows/block-duplicate-cosync-pr.yml

  • Blocks/warns when another co-sync/* PR is already open against main

• Updates scripts/code_ocean_sync.sh

  • Supports any module with modules/<module>/runtime/
  • Keeps portable fallback when rsync is unavailable
  • Copies auto-cosync-pr.yml into outbound co/<module> exports
  • Excludes .github/ from reverse sync

• Updates documentation

  • Makes the [sync] automation the primary workflow
  • Keeps manual reverse sync as a fallback
  • Updates the Mermaid/Lucidchart diagram

Validation

• bash -n scripts/code_ocean_sync.sh
• YAML parse check for both new workflows
• Rscript tests/test-module-contract.R
• modules/volcano/runtime/tests/test_run_small.sh
• Tested outbound/reverse sync dry-runs, including portable fallback mode

Note

After this merges to main, each persistent co/<module> export branch should be refreshed once so it receives .github/workflows/auto-cosync-pr.yml. That enables future [sync] commits from Code Ocean to trigger automation.

Closes #5