Problem

1. When scanning the repository, certain paths are not indexed.
2. Searching the logs show no error in logs.
3. When viewing the repository via Administration >> Repository List >> View (next to your repository), the repository definition as well as any Includes or Excludes.

Diagnosis

Diagnostic Steps

Check Administration >> Repository Defaults for an incorrect Includes or Excludes in the defaults. This will affect your repository.

Cause

Repository default settings apply to all repositories, however viewing the repository directly via Administration >> Repository List >> View, will not reveal these rules, thus it is easily cause confusion.

Resolution

Remove the incorrect Includes and Excludes from Administration >> Repository Defaults.
There is an improvement open which once implemented will eliminate this confusion:

FE-2654 - Getting issue details... STATUS