As migrations are stored in .wappler/migrations/ they are excluded by default from git.
That also happens for routes and theme variables which are probably files we want under version control.
Wouldn’t an updated .gitignore approach just include .wappler/targets and .wappler/project.json?
In my projects, I have removed evrything with the exception of node_modules. Works great.
Well in normal private repositories you should indeed always commit the .wappler folder as well. Specially if you are working on multiple computers or in a team.
Default we added it to gitignore so that people don’t go and post all their security settings publicly on github 
I don’t know your setup, but projects.json includes database passwords
You probably should ignore that file.
I do that same as @ben and remove .wappler from the .gitignore file.
But, it would be great if database and FTP passwords could be stored in a separate file which could be ignored for added security. That said, I always work with private repos so I’m not desperately bothered.