feat: override files, but don't clear dir on `generate-repo` command

[MihalyToth20]

Currently the generate-repo command first clears out the target directory and then pulls and writes all xanoscript and accompanying json files in there. Which means that adding extra files alongside those files will be cleared on next pull.

Expected: to override

• *.freezed.xs files
• the README.mds
• the JSON-definitions

But to keep the rest of the files untouched. This also has to cover for those files that fall into the above mentioned categories and are not found, those should be deleted. This probably requires a more thorough fs traversal...