Use TEXINPUTS for file search path. Files \inputed not using a path relative to root, but a location in TEXINPUTS won't be picked up by TexLab. This causes two things:

1. no path autocomplete;
2. bib resources not picked up and causing many Undefined references false positives.

In my personal use case, I'm setting TEXINPUTS in my latexmkrc file using:

ensure_path("TEXINPUTS", "src//");

Maybe there is a way to get the file search paths from latexmk somehow?