Fix path flattening collisions and make runfiles resolution deterministic in make_corpus_dir

[jmestwa-coder]

Summary

Fixes path flattening collisions and makes runfiles resolution deterministic in make_corpus_dir.

---

Problem

• Different inputs could map to the same output (e.g., dir/../a.txt vs a.txt, ./a.txt vs dot-a.txt)
• Runfiles resolution could pick the wrong script depending on manifest order

---

Solution

• Preserve input path structure during flattening (no unintended normalization)
• Ensure unique output names using deterministic suffixing and fallback aliasing
• Make runfiles resolution deterministic:
  • prefer workspace entries
  • use _main only as fallback
  • ignore unrelated repos

---

Result

• Distinct inputs always produce distinct outputs
• No silent collisions or overwrites
• Deterministic behavior across runfiles and manifest modes

---

Tests

• Added coverage for path edge cases and collision scenarios
• Verified runfiles resolution across:
  • TEST_SRCDIR
  • RUNFILES_DIR
  • RUNFILES_MANIFEST_FILE
  • multi-repo manifests

[jmestwa-coder]

Hi @fmeum, @simonresch Can you kindly review this PR. Thank you!

[simonresch]

The only caller of make_corpus_dir is in fuzzing_corpus where https://github.com/bazel-contrib/rules_fuzzing/blob/main/fuzzing/private/common.bzl#L86 calls it with a list of workspace relative, cleaned list of files. Where is the potential for dir/../a.txt vs a.txt, ./a.txt ambiguity?

Could you make sure the added test passes? You can run it with the command bazel test //fuzzing/tools:make_corpus_dir_test.