Clean up the database if it will be uploaded

[henrymercer]

Even with --expect-discarded-cache, intermediate results may still be written to the database if there is high RAM pressure. So clean up the database if we will upload it.

There are a couple of approaches to doing this. I went with moving the cleanup into the upload stage to avoid needing to pull out separate logic about whether the upload should take place or not (and potentially needing to run this logic twice). This does make the cleanup slightly less transparent — I added comments and don't think this is too problematic but feedback welcome.

Merge / deployment checklist

• Confirm this change is backwards compatible with existing workflows.
• Confirm the readme has been updated if necessary.
• Confirm the changelog has been updated if necessary.

[Copilot]

Pull Request Overview

This PR refactors database cleanup to ensure databases are properly cleaned before upload operations. The primary purpose is to address the issue where intermediate results may still be written to databases even with --expect-discarded-cache when there is high RAM pressure, requiring cleanup before uploading.

Key changes include:

• Moving database cleanup logic from a separate stage into the respective upload functions
• Removing the standalone runCleanup function and cleanupLevel parameter from runQueries
• Adding databaseCleanupCluster method to the CodeQL interface for cleaning all databases in a cluster

Reviewed Changes

Copilot reviewed 14 out of 21 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/codeql.ts	Adds new databaseCleanupCluster method to CodeQL interface and implementation
src/database-upload.ts	Integrates database cleanup directly into upload flow with "clear" level cleanup
src/overlay-database-utils.ts	Adds database cleanup at "overlay" level before caching overlay databases
src/analyze.ts	Removes standalone cleanup function and cleanupLevel parameter from runQueries
src/analyze-action.ts	Updates workflow to handle cleanup-level input deprecation and reorders upload operations
src/database-upload.test.ts	Updates tests to accommodate new CodeQL parameter and mock cleanup method
src/analyze.test.ts	Removes cleanupLevel parameter from test calls

Comments suppressed due to low confidence (1)

src/database-upload.ts:19

• Adding the codeql parameter to this function is a breaking change to the API. Consider documenting this breaking change in the PR description or changelog to help consumers of this function.

  repositoryNwo: RepositoryNwo,
  codeql: CodeQL,
  config: Config,
  apiDetails: GitHubApiDetails,
  logger: Logger,
): Promise<void> {

[Copilot]

The cleanup-level deprecation warning has been moved earlier in the function but the logic is duplicated - this same warning appears in the original location. Consider removing this duplication to avoid confusing users with multiple identical warnings.

Suggested change

[cklin]

Shall we remove the databaseCleanup() function, since it is now replaced by databaseCleanupCluster() and no longer used?

[cklin]

Thanks for the code update!