Use the correct ignore files regex method for the java frontend

[prabhu]

withDefaultIgnoredFilesRegex doesn't really work with the java frontend due to this line.

ignoredDefaultRegex = Option(JavaSrc2Cpg.DefaultIgnoredFilesRegex),
ignoredFilesRegex = Option(config.ignoredFilesRegex),
ignoredFilesPath = Option(config.ignoredFiles)

Switching to withIgnoredFilesRegex helps fix the issue reported in cdxgen.

[gemini-code-assist]

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Summary of Changes

This pull request addresses an issue where the withDefaultIgnoredFilesRegex method was not working as expected with the Java frontend due to the order in which the ignore file regexes were being applied. The change replaces withDefaultIgnoredFilesRegex with withIgnoredFilesRegex and updates the regex to correctly ignore target and build directories.

Highlights

• Bug Fix: Fixes an issue where default ignored files regex was not working correctly for the Java frontend.
• Regex Update: Updates the ignored files regex to correctly ignore target and build directories.
• Method Replacement: Replaces withDefaultIgnoredFilesRegex with withIgnoredFilesRegex to ensure correct application of ignore rules.

Changelog

• src/main/scala/io/appthreat/atom/Atom.scala
  • Replaced withDefaultIgnoredFilesRegex with withIgnoredFilesRegex.
  • Updated the ignored files regex to .*(target|build)/(generated|intermediates|outputs|tmp).*.

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