pyls cannot be initialized if I closed atom with clicking title bar last time

Ok, here is the thing. If I close atom with clicking title bar, next time, when I have to close all files, and re-open them, or I cannot connect to pyls. However if I close atom with cmd+w, then next time all files can automatically connect to pyls.

OS: mac OS and everything is last version.

No file, test, or code entry point is named. Reproduce the macOS behavior by closing Atom from the title bar versus cmd+w, then trace pyls initialization and reconnection; done means files connect to pyls after reopening through both paths.

Written by the indexing model from the issue text.