We personally use google docs for organizing large RPs.

Ignoring the various collab/CS/note-things-down docs, our doc list for just one RP counts 44 docs.
many of those are no longer in active use, but they were relevant for the crafting of the RP.

The important thing to do when you use something like google drive for organizing a massive RP is to have a system in your folder and in naming docs. In our case, we used numbers in front of doc names, plus an archive.

01-19 = various work docs, like RP core plan, interest check a few workbenches and such. This category also holds the doc containing the first/zeroth posts for the RP thread. 
20-29 = GM sheets
30-39 = Side stories set outside the RP's main continuity
40-49 = Lore docs

An alternate organization is to use multiple subfolders, but we found that numbers made it easier to find the right doc when we needed it.

This setup was made for an RP with three GMs.