Add Go Docstrings and Refactor matrix to tim

[google-labs-jules]

This change adds comprehensive Go docstrings with examples to all packages in the project, aiming for 100% documentation coverage. It also includes a significant refactoring, renaming the pkg/matrix package to pkg/tim and updating all related terminology (e.g., "Terminal Isolation Matrix" to "TIM") throughout the codebase. This includes updates to command-line flags, help text, test files, and examples for consistency.

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PR created automatically by Jules for task 4150815874004671938 started by @Snider

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[codecov]

Codecov Report

❌ Patch coverage is 41.46341% with 24 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
cmd/all.go	18.18%	6 Missing and 3 partials ⚠️
cmd/collect_github_repo.go	16.66%	3 Missing and 2 partials ⚠️
cmd/collect_pwa.go	16.66%	5 Missing ⚠️
cmd/collect_website.go	16.66%	3 Missing and 2 partials ⚠️

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