Does anybody have a better idea on how to fix these two problems? Or a better way to write the rules above for this?
zanata-cli does not look outside of srcdir. So the solution would be target whichever directory that is in higher structure.
I think your solution is the best approach so far to solve this issue.
Alex, is there a way to not lose the content when this change is done since it will rename the translation files?
The renaming of files will definitely lose their translation content (Zanata will mark the document obsolete).
If renaming of files happens, then we will need to do zanata:pull, rename all files and zanata:push as you suggested.
This process shouldn't be a problem if there's constant syncing of translation files (as backup) and we can always attached the last pulled translation files.
From Zanata point of view, there is actually a feature to copy translations however I don't recommend to use it unless you're really sure.