IntelliJ Dynamically Created Folders For Installation Package Maker Help

So, we have a big old application that uses lots of big old discrete data-sets. Inside our big old application, we have a folder called installation-package-maker responsible for making various distributions of our software and data. So basically our package maker has various tools in it for creating launchers, installers, code signing, autostart files, etc. etc.... and then it has various stagging folders for pulling datasets in locally and the final assembled/reduced/obfuscated application too.

So basically we have all these 'pieces' of installation packages and we have various 'assemblers' to bring all these pieces together for a large variety of distributions options. Note, a lot of these 'pieces' create folders dynamically. Everything works great except for these issues:

• When I pull in a huge dataset or the huge application into it's staging area, IntelliJ spends the next 2 hours indexing... not the usual background indexing either, I can't do anything while it's indexing, everything is locked and a popup keeps coming up saying updating indices. This creates a pretty big problem, because now when I search everywhere it searches in the main development application AND the staging area, so search results are duplicated. Additionally since we don't want to push these staging folders to our main git for obvious reasons these staging folders are often dynamically created, because git doesn't store empty folders (which is weird)... so really how would I tell intelliJ not to index?
• Another issue is that we pull our application (and datasets soon) into the staging area from 1 of 2 repos, QA and Production... but this results in a git within a git. So when I pull for the entire development project, it pulls these staging repos too.... when I 'update' the staging area from git, it tends to update the development master project too (once it actually removed all my changes too).

So the questions:

• How do I stop IntelliJ from indexing dynamically created folders... considering I'm not the only one using the tool... ideally if I could add an ignore_indexing file to these folders that would be great, because then the folders would end up being pushed to git since they aren't empty and anyone else using this wouldn't suffer from the indexing issue.
• What's the best way to deal with this stagging git within a development git?