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Rebuild: Works for entire projects, only. Clears the index and indexes the files from scratch. When cancelled it leaves you with an empty or partial index.

Update with Modified Files: Works on a resource selection. Checks on individual files whether the timestamp or the scanner-config has been changed and updates the index for the changed files.

Freshen All Files: Works on a resource selection. Updates the selected files in the index. The index is not cleared, it is safe to cancel the operation.

cdt's indexer options explained

c++ - Clean Eclipse Index, it is out of sync with code - Stack Overflow

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