update readme
use relative path for paths.mk
add some more ignored files using regex to .gitignore
fix generate_deps to work on a mac
Merge pull request #2 from EDmodel/small_tweaks

some small tweaks to setup, no code changes.
merged Afshin's changes and resolved conflicts
Merge pull request #4 from mdietze/master

Merge Afshin's changes: fixing compilation errors
The model finishes initialization and starts simulating but crashes in first time step.