LogSeq folder as child of repo breaks commit and push

[thecapedcoder]

If you have your LogSeq folder inside of a repo, and not the repo itself, attempting to push creates a .git file (not folder) in the LoqSeq folder with a reference to the directory it is in. This is forcing git to treat the folder like a submodule and ignore the changes to the subfolder.

Steps to repro:

1. Checkout a repo
2. Create a LoqSeq graph stored in a sub folder of that repo
3. Make change
4. Commit and push, "No changes to push".
5. .git file now exists in LogSeq folder.

In troubleshooting I ran all the commands, as run by the plugin, I wasn't able to produce this with git exclusively so it does seem to be something happening in the plugin itself as I also cannot reproduce without the plugin (no plugin, no .git file).