TL;DR: Move your .git folders out of ~/Code into ~/Git/[reponame]. Use ln -s or plain text .git file[1].
I have my code folders in Dropbox on OSX but I believe my process should work for you. I work in node and have a number of monorepos with nested node_modules folders. I run my idempotent dev-files.command script [2] with or without "--nono" in any monorepo and it handles the entire git aliasing and dropbox folder ignore for node_modules process. I use --nono if I ever need to clear out all of the node_modules and do a fresh pnpm install.
I have my code folders in Dropbox on OSX but I believe my process should work for you. I work in node and have a number of monorepos with nested node_modules folders. I run my idempotent dev-files.command script [2] with or without "--nono" in any monorepo and it handles the entire git aliasing and dropbox folder ignore for node_modules process. I use --nono if I ever need to clear out all of the node_modules and do a fresh pnpm install.
1. https://git-scm.com/docs/gitrepository-layout
2. https://gist.github.com/chiragmehta/a41bd33356b6a2f84075d23d...