fix: improve logic for --all-packages flag

[Ly-Joey]

Updated logic so that unscannable packages are still filtered for vulnerabilities and license matching, but they will be re-added to the final JSON result if the --all-packages flag is passed in.

Also updated docs to clarify the order of precedence between --all-packages flag and PackageOverrides actions in the config file.

Fixes #2157

[another-rex]

Nice! LGTM

[another-rex]

Test error seems to be from a snapshot update, just run tests with UPDATE_SNAPS=true and it should be fixed.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 76.47059% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 67.91%. Comparing base (c3eecf4) to head (4ec427e).

Files with missing lines	Patch %	Lines
pkg/osvscanner/filter.go	71.42%	2 Missing ⚠️
pkg/osvscanner/osvscanner.go	66.66%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2311      +/-   ##
==========================================
- Coverage   67.95%   67.91%   -0.05%     
==========================================
  Files         172      172              
  Lines       12821    12836      +15     
==========================================
+ Hits         8712     8717       +5     
- Misses       3437     3446       +9     
- Partials      672      673       +1     

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