Add native Stone manifest support

[aaronsky]

Description

Adds the native Stone manifest support that xplat needs:

• --output-manifest to report generated output paths without writing generated file contents.
• Default validation that backend writes stay under the configured output root.
• --expected-output-manifest to compare generated output paths against a checked manifest.
• --recursive so directory spec arguments expand to .stone files.

This PR now includes the landed middle stack changes so the remaining stack can land cleanly.

Checklist

General Contributing

• Have you read the Code of Conduct and signed the CLA?

Is This a Code Change?

• Non-code related change (markdown/git settings etc)
• Code Change
• Example/Test Code Change

Validation

• Have you ran tox?
• Do the tests pass?

Verification run directly with the CI lint/test steps:

• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with flake8==5.0.4 --with pylint flake8 setup.py example stone test
• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with flake8==5.0.4 --with pylint --with setuptools pylint --rcfile=.pylintrc setup.py example stone test
• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with pytest --with mock pytest
• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with enum34 --with mypy --with types-six ./mypy-run.sh

[codecov]

Codecov Report

❌ Patch coverage is 69.00000% with 31 lines in your changes missing coverage. Please review.
✅ Project coverage is 51.34%. Comparing base (1ad079b) to head (fb99efd).
⚠️ Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
stone/cli.py	64.44%	15 Missing and 1 partial ⚠️
stone/backends/obj_c_types.py	0.00%	7 Missing ⚠️
stone/backends/swift_types.py	0.00%	3 Missing ⚠️
stone/backend.py	94.44%	1 Missing and 1 partial ⚠️
stone/compiler.py	66.66%	1 Missing and 1 partial ⚠️
stone/backends/swift.py	66.66%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #359      +/-   ##
==========================================
+ Coverage   49.98%   51.34%   +1.35%     
==========================================
  Files          37       37              
  Lines        8808     8870      +62     
  Branches     1892     1911      +19     
==========================================
+ Hits         4403     4554     +151     
+ Misses       4087     3974     -113     
- Partials      318      342      +24     

Flag	Coverage Δ
unit	51.34% <69.00%> (+1.35%)	⬆️

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