master is red: the 09-30 batch merge reverted #146, #160 and #161 and overwrote #138 #165

What is broken

master (7f1ff93) is red: every Test (Python 3.x, *) leg of CI fails, so CI Gate fails. Reproduced locally on Ubuntu 20.04 (WSL2), Python 3.12.14: pytest tests reports 25 failures and 1 collection error.

Why

The 09-30 batch merge resolved two overlaps by dropping already-merged work:

1. Merge of refactor: move executable output layout out of Ninja backend #141 (40d5a65) replaced ebuild/cli/commands.py with a copy that predates three merged PRs. Ignoring line endings, git diff 40d5a65^1 40d5a65 -- ebuild/cli/commands.py removes:
   • feat(ebuild): add runner args support for flash tools #161 (runner args): _resolve_runner_args, flash --config, --no-runner-args, passthrough args. Result: tests/unit/cli/test_commands_utils.py cannot be imported, and 17 test_flash_args.py cases fail with No such option '--config'.
   • fix(packages): read ebuild.lock back, so it pins what it records #146 (lockfile read-back): the lock is no longer read before resolving, and a corrupt lock is no longer reported. Result: 2 test_lockfile_cli.py failures.
   • fix(ebuild): use ninja_command() in ebuild build #160 (ninja_command()): build goes back to hard-coding python -m ninja. Result: test_build_uses_the_path_binary_when_present fails.
2. Merge of fix(ebuild): recreate static archives to remove stale objects #137 (18b3ee5) replaced fix(ebuild): recreate static archives on rebuild (stub-tested) #138's recreate_archive.py archive rule with an inline python -c command. fix(ebuild): recreate static archives on rebuild (stub-tested) #138's tests and helper are still in the tree, so 3 TestStaticArchiveRecreation tests fail.
3. The archive-member tests from fix(ebuild): recreate static archives to remove stale objects #137/fix(ebuild): recreate static archives on rebuild (stub-tested) #138 expect keep.o. Since fix: avoid ninja object path collisions #133, _object_path writes keep.c.o, so those tests are now wrong.
4. ruff check . reports 13 trailing-whitespace errors in tests/unit/cli/test_commands_utils.py (from feat(ebuild): add runner args support for flash tools #161).

Expected

Put back the dropped work without undoing #141's real change, which moves executable_output_path to ebuild/build/layout.py. After that, pytest tests, ruff check ., yamllint ., and the CI mypy command should all pass.