gc.sh: rewrite Git repo cleaning.

- improve find logic (find also bare repos) and search on all levels
- ditch git pull-update and selection NO_PULL/NO_GC flags
- also clean reflogs and explicitly prune repositories
Makefile.pregenerate: refactor PREGENERATE DB, improve marker update logic of PREGENERATE BUILD-DB.

- PREGENERATE DB: touch marker after generation
- PREGENERATE BUILD-DB: touch marker with current time (all modifications will
surely happen after the generation is completed)