When MATLAB starts, it will look for a pathdef.m file in its startup directory. It should not be edited - leave the default MATLAB path containing only MATLAB native toolboxes. The rest should be configured dynamically, as explained below/

Start up folder (in the MATLAB icon | Properties | Start in ) (e.g. D:\Sources\MATLAB) allows controlling different paths and other settings via startup.m file placed in the folder, e.g.:

disp('Welcome to MATLAB2014');
set_sources_path;
edit;
EditorMacro('Alt-Control-h', @ig_createHeaderComment_dag);
dbstop if error

See https://github.com/igorkagan/matlab_config for example startup.m that allows excluding .git folders from the path.