Feature/eng 452 remove functions to trackcsv

[silverboyir]

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[Copilot]

Pull request overview

This PR implements a significant architectural change to make the verilib-cli tool more resilient by making previously required dependencies optional. The create command no longer requires functions_to_track.csv or the Python analysis script to succeed, and other commands will auto-create missing configuration files rather than failing. This enables a graceful degradation pattern where commands can continue with reduced functionality when optional dependencies are absent.

Changes:

• Made functions_to_track.csv optional in the create command; when absent, the script tracks all functions by default (if script runs)
• Made analyze_verus_specs_proofs.py script optional; create command continues without structure files if script is absent or fails
• Added auto-creation of default config.json when missing, allowing commands to proceed rather than failing

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
src/commands/create.rs	Refactored to make seed path optional, handle script absence gracefully via try_run_analyze_verus_specs_proofs, and support both project and bundled script locations
src/structure/config.rs	Added DEFAULT_CONFIG_JSON constant and logic to auto-create config when missing in ConfigPaths::load
src/commands/atomize.rs	Added has_md_files check to write empty stubs.json when no structure files exist, preventing stubify failures
tests/structure_commands_test.rs	Updated test names and assertions to reflect new optional behavior, removed fallback seed checks
README.md	Updated documentation to clarify that script and CSV file are now optional

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[astefano]

We no longer need analyze_verus_specs_proofs.py.
We shouldn't commit functions_to_track.csv (the one in this repo represents the functions in this repo!).

Also, i notice docker stuff in structure; structure is supposed to be about managing verification structure files, these are data-layer concerns. We shouldn't leak docker stuff inside structure. There's this issue documenting it: #17.

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