feat(clean): group Python bytecode cleanup by project root

[byronwang2005]

Summary

• Group Python bytecode cache cleanup output by detected project root instead of printing one line per __pycache__ directory.
• Preserve grouped dry-run export entries and skip/accounting behavior for protected or whitelisted Python cache directories.
• Process project-cache scan results per scan root so output appears incrementally instead of arriving in one large batch.
• Keep existing Next.js and Flutter project-cache cleanup behavior compatible with the new flow.

Safety Review

• Does this change affect cleanup, uninstall, optimize, installer, remove, analyze delete, update, or install behavior?
• Yes. It affects clean behavior for project cache cleanup, specifically Python __pycache__ handling and the timing/format of project-cache output.
• Does this change affect path validation, protected directories, symlink handling, sudo boundaries, or release/install integrity?
• It affects protected-directory and whitelist handling inside grouped Python cache cleanup.
• New boundary/risk change:
• Grouped Python cleanup now preserves the same protected-path and whitelist skip behavior as the previous per-directory flow by updating skip counters and writing SKIPPED operation logs.
• Dry-run behavior is preserved by continuing to register/export concrete cleanup targets instead of only showing grouped summaries.
• No changes were made to path validation rules, symlink handling, sudo boundaries, installer/release integrity, or destructive scope beyond the existing __pycache__ targets.

Tests

• Automated tests run:
• ./scripts/check.sh
• ./scripts/test.sh (current repo still has unrelated existing failures in tests/cli.bats for mo status --json)
• Targeted tests run during development:
• bats tests/clean_system_caches.bats -f "clean_project_caches completes without errors"
• bats tests/clean_system_caches.bats -f "clean_project_caches groups pycache directories by project root"
• bats tests/clean_system_caches.bats -f "clean_project_caches pycache dry-run exports grouped targets and counts skips"
• bats tests/clean_dev_caches.bats -f "clean_project_caches cleans flutter .dart_tool and build directories"
• Manual checks:
• Ran ./mo clean --dry-run globally and verified Python bytecode cleanup now prints grouped project-root summaries.
• Inspected generated dry-run behavior and sampled real __pycache__ directories to confirm several 0B dry cases were due to empty cache directories, not size-calculation regression.

Safety-related changes

• None.

[byronwang2005]

May close issue #633.

[chatgpt-codex-connector]

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[tw93]

@byronwang2005 LGTM! This directly addresses a well-reported pain point (#633), grouping by project root turns 1000+ noisy lines into clean per-project summaries. The decomposition is solid and the existing safety checks (whitelist, protect path, dry-run) are all preserved.

A couple of minor things worth tidying up in a follow-up if you have time:

• flush_python_bytecode_cache_group() is defined but never called — can be removed
• The eval in flush_python_group_if_needed() works fine but could be simplified by passing array elements directly instead of the array name
• rm -f on temp files is a minor convention deviation (project prefers safe_* helpers for all removals)

None of these are blockers. Thanks for tackling this one!