I have manually compiled vim following the instructions on https://github.com/Valloric/YouCompleteMe/wiki/Building-Vim-from-source. I changed the configure step to include --prefix=/usr/local and then ran make with make VIMRUNTIMEDIR=/usr/local/share/vim/vim80.
Everything seems to work great. I see the vim/ directory in /usr/local/share and it even is set as the "default" version of vim.
I've followed several different methods: holding, and using --set-selections and according to this answer installing into /usr/local should be safe from having my compiled version of vim from being overwritten. However, every time I run apt-get upgrade I lose my version of vim.
What's going on?