Merge pull request #48 from joelkuiper/develop

Fix stupid mistakes
Minor fixes for 0.1
Don't run "long" chain in example; remove objects
Update READMEs to reflect current situation

 * Add r-code README
Depend on Java 1.5 for R package

 * Change system dependency in DESCRIPTION
 * Add jaxb-impl dependency to mtc-model
 * Change top-level POM to require Java 1.5
 * Change mtc-gui POM to require Java 1.6
Version to 0.14.2; depend on common 0.5.6
Remove @Override for JDK 1.5 compatibility
Fix failing test

 * AbsoluteOneCenterTest treated undefined outcome as defined.
Fix non-deterministic orderings (JDK 1.5)
Implement equals/hashCode for Study
r-code: detect version in Makefile
r-code: bump version for JDK 1.5 fixes
Do not use j.model in mtc.parameters (fixed #610)

Replaced mtc.parameters(j.model) by an S3 method that is defined on mtc.model, mtc.result, and jobjRef
Bump version, add note
Fix starting values generation (fixed #609)

 - Adhere to RSM paper for random effects standard deviation starting value.
GeMTC version to 0.14.3 and bump R package version
Don't try to load "YADAS" package (fix #615)
Rename 'sd' to 'std.dev' (fix #617)
Sanity check the mtc.network (fix #616)
mtc.network fixes (fix #611, #618)

 - mtc.network.as.java explicitly sets names(treatments)
 - mtc.network preprocesses data and treatments