fix: Isolate Bazel sources from CMake generation

[yuefdev]

Running python scripts/generate_build_files.py --bazel --cmake adds the Bazel-only //utils:CommonGraphOptions.cpp label to the generated CMake source list. The Bazel branch mutates graph_files, which is then reused for CMake generation.

Build a separate Bazel graph-source list so combined generation produces exactly the same files as separate invocations. The production change is two lines, accompanied by subprocess regression tests.

Validation:

• Both regression tests pass with Python 3.10.21, including both flag orders, byte-for-byte comparisons against separate generation, and preservation of the Bazel utility label and graph sources. Before the fix, three assertions failed.
• Tests pass on this independent main-based branch as well as when combined locally with fix: Make contributor checks work on Windows #1310.
• Contributor hooks and pre-push checks pass with the Windows tooling fixes in fix: Make contributor checks work on Windows #1310. The unmodified main tooling still fails locally on Windows as described there; this PR contains only the generator fix and its test file.
• Tests exercise the real generator and repository filelist in temporary directories. No full CMake/Bazel build or Arm inference was run.