To manually delete the repository cache and trigger the reindexing of the repository, the following steps can be performed against the repository in your instance.

1. Navigate to Fisheye administration page Repository Settings > Repositories
2. Stop the affected repository by selecting from the dropdown option in the Action column
3. Shutdown Fisheye instance
4. Backup and delete the cache folder of the affected repository at FISHEYE_INST/var/cache/MyRepoName directory
5. Start Fisheye instance
6. Start the repository from the dropdown option in the Action column and this will trigger the reindexing of the repository

This can also be achieved through Fisheye's User Interface by following the below steps:

1. Navigate to Fisheye administration page Repository Settings > Repositories
2. Select the repository under the Name column
3. Select the Maintenance link
4. Select Start for Re-clone and Re-index