Unity project suddenly dependent on Library folder

My partner and I have been working on an iOS game in Unity. We are using GitHub for version control and have had only the Assets and ProjectSettings folders in the repo. We use visible meta data files. We ignored the Library as per usual.

However, at some point unknown to us, the project became corrupted in some way and now has to rely on the Library. We only figured this out when we deleted our local copies and attempted to reclone from the GitHub repo only to find the project was not loading major plugins our game relies on including PlayMaker and SVG Importer - effectively breaking the project. Basically, rebuilding the Library - a standard thing in version control for Unity projects - corrupts the project.

We got around this issue by copying a Library from an older local build and now we version control this. But this is really no the best workflow because there are hundreds of metadata files that are now under version control when they shouldn't have to be. Also, things like our personal editor window arrangement are now synched between us.

My question is how can we fix our project so that it is no longer reliant on the Library? What could have made it reliant on the Library in the first place? Does this have something to do with metadata files?

Found a reddit post with a similar problem: https://www.reddit.com/r/Unity3D/comments/3h72vd/deleted_librarymetadata_folder_unity5_corrupted/

Have not found any similar cases in Unity forums. Any insight would be appreciated.