Documentation update: convert README to markdown, restructure READMEs

README -> README.md: main README is now in markdown format and contains
information only about typical use cases (building and parsing). Pointers
to the other READMEs added in place of the cuts for those interested
in retraining.

second-stage/README-retrain.md: Information about retraining the reranker
has been pulled out here.

first-stage/README: minor updates about thread safety
Use cvlm-lbfgs in more Makefiles/scripts
Updated the ESTIMATOR* variables to use cvlm-lbfgs.

Thanks to Marten Van Schijndel for pointing this out!