Feat: v1 fix with version provenance for requirements.txt projects

[lili2311]

• Follows CONTRIBUTING rules

What does this PR do?

• stop skipping files with -r directive (continue not support -c for now)
• extract all relevant files referenced via -r and apply fixes with this context in mind
• sometimes we may have already fixed a certain file that snyk test will send to be fixed because it was included by another file.
• snyk test does not today skip testing files that have already been tested because they are essentially included as part of other tests, however snyk fix needs to separate this so we do not try to apply fixes again to a fixed file.
• call out previously fixed in the output as we bail to apply changes again there.

Where should the reviewer start?

How should this be manually tested?

• git rebase feat/snyk-fix Feat: snyk fix v1 (Python) in behind FF #1707
• cd packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed && snyk fix --all-projects --org=org-with-ff

Any background context you want to provide?

The logic behind the fix of grouped files is as follows:

• for each sorted directory
• fix all entities in the current directory
• for each entity extract provenance information (find and parse all files that are included via -r)
• apply all upgrades first across the related files
• apply the remaining fixes as pins in the entry file (aka the file that was tested via snyk test first)
• keep track of files that we applied fixes in and skip fixing it if previously fixed

Screenshots

[github-actions]

Expected release notes (by @lili2311)

features:
v1 support for previously fixed reqs.txt (b286418)
basic pip fix -r support (0384020)
include pins optionally (f94c558)
do not skip files with -r directive (66ca77a)
fix individual file with provenance (6e84322)

others (will not be included in Semantic-Release notes):
fix individual reqs manifest (bc44f9a)

• I hereby acknowledge these release notes are 🥙 AWESOME 🥙