refactor(coverage): rename JavaSrcDirFinder to SrcDirFinder and add CLI options

[brynary]

Summary

• Rename java_src_dirs to src_search_dirs in Settings for more generic naming
• Rename JavaSrcDirFinder to SrcDirFinder (including file rename)
• Update user-facing output from "Discovered Java source directories" to "Source search directories"
• Add --add-src-dir CLI option to manually specify source directories (takes precedence over auto-discovered)
• Add --remove-src-dir CLI option to exclude directories from the search list
• Add warning when a file is found in multiple source directories

Test plan

• All existing tests pass (230 unit tests + 12 integration tests)
• Manual test with --add-src-dir option
• Manual test with --remove-src-dir option
• Manual test combining --add-src-dir with --discover-java-src-dirs

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[Copilot]

Pull request overview

This PR refactors the Java source directory finder to be more generic, renaming it to SrcDirFinder and adding new CLI options for manually managing source search directories. The changes support multiple source directories and add warning capabilities when files are found in multiple locations.

Key changes:

• Renamed JavaSrcDirFinder to SrcDirFinder and java_src_dirs to src_search_dirs for more generic naming
• Added --add-src-dir and --remove-src-dir CLI options for manual directory management
• Implemented warnings when files are found in multiple source directories (uses first match)

Reviewed changes

Copilot reviewed 5 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
qlty-coverage/src/transformer.rs	Refactored PrependSrcDir::transform to detect and warn when files exist in multiple source directories
qlty-coverage/src/src_dir_finder.rs	Renamed struct from JavaSrcDirFinder to SrcDirFinder with updated test references
qlty-coverage/src/publish/settings.rs	Renamed field from java_src_dirs to src_search_dirs
qlty-coverage/src/publish/planner.rs	Updated to use src_search_dirs instead of java_src_dirs
qlty-coverage/src/lib.rs	Updated module and export names from java_src_dir_finder to src_dir_finder
qlty-cli/tests/cmd/coverage/discover_java_src_dirs.stderr	Updated test output from "Discovered Java source directories" to "Source search directories"
qlty-cli/src/commands/coverage/utils.rs	Updated output message and logic to display source search directories
qlty-cli/src/commands/coverage/publish.rs	Added --add-src-dir and --remove-src-dir CLI options with implementation logic and updated warning messages

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[qltysh]

Coverage Impact - macos-15

⬇️ Merging this pull request will decrease total coverage on main by 0.01%.

Code Coverage of Modified Files (5)

Rating	File	% Diff	Uncovered Line #s
	qlty-cli/src/commands/coverage/publish.rs	52.9%	272-277, 340, 342
	qlty-coverage/src/publish/planner.rs	100.0%
	qlty-coverage/src/transformer.rs	95.5%	323, 325
	qlty-cli/src/commands/coverage/utils.rs	100.0%
	qlty-coverage/src/src_dir_finder.rs	100.0%
	Total	91.5%

🚦 See full report on Qlty Cloud »

🛟 Help

• Diff Coverage: Coverage for added or modified lines of code (excludes deleted files). Learn more.

• Total Coverage: Coverage for the whole repository, calculated as the sum of all File Coverage. Learn more.

• File Coverage: Covered Lines divided by Covered Lines plus Missed Lines. (Excludes non-executable lines including blank lines and comments.)

  • Indirect Changes: Changes to File Coverage for files that were not modified in this PR. Learn more.

[qltysh]

Coverage Impact - ubuntu-latest

⬇️ Merging this pull request will decrease total coverage on main by 0.01%.

Code Coverage of Modified Files (5)

Rating	File	% Diff	Uncovered Line #s
	qlty-cli/src/commands/coverage/publish.rs	52.9%	272-277, 340, 342
	qlty-coverage/src/publish/planner.rs	100.0%
	qlty-coverage/src/transformer.rs	95.5%	323, 325
	qlty-cli/src/commands/coverage/utils.rs	100.0%
	qlty-coverage/src/src_dir_finder.rs	100.0%
	Total	91.5%

🚦 See full report on Qlty Cloud »

🛟 Help

• Diff Coverage: Coverage for added or modified lines of code (excludes deleted files). Learn more.

• Total Coverage: Coverage for the whole repository, calculated as the sum of all File Coverage. Learn more.

• File Coverage: Covered Lines divided by Covered Lines plus Missed Lines. (Excludes non-executable lines including blank lines and comments.)

  • Indirect Changes: Changes to File Coverage for files that were not modified in this PR. Learn more.