I use some .sty-files that are not part of texlive and want to have them in a subdirectory of the folder with my main.tex. I used the following line to load the package:
Simply put line below before the call to pdflatex (or latex) in your makefile or build script:
export TEXINPUTS=".:./sty:"
Then reference your package as:
\usepackage{prettythesis}