Adds support for dot-prefixed paths in git

- in `flux bootstrap` and `flux create kustomization` etc.
- E.g. for example `--path=.flux` should work now
- Previous behaviour is to strip off any leading "." and leave you with
  "./flux" in the kustomizations / folder structure generated by `flux
  bootstrap`

Signed-off-by: Simon Howe <footless@gmail.com>