Keep a repository's own settings in a cached scan

A scanned repository is read back from the cached list under the global
settings, so a setting that only differed from them by being off, or by
naming the default value, came back as the global one. branch-sort was
written only for age, per-path module links not at all, and a filter a
repository turned off left no line behind.

Writing an empty value for a filter turned off makes the list depend on
whether each global filter is set, so the scan key names that too.

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