regenerated doc (for v3.2.0)

Merge pull request QuEST-Kit#240 from QuEST-Kit/develop

v3.1.1

removing superfluous mainpage from doc

Merge pull request QuEST-Kit#212 from QuEST-Kit/develop

Bug fixes

generated v3 doc

Update README.md

Merge pull request QuEST-Kit#96 from QuEST-Kit/masterBugFix_mpiSeeding

mpi version of seeding function used wrong data type.

Manually restoring aux unit test files

I can't explain why these weren't brought forward with the merge from dev into master

Updating version number to v1.1.0 in README

fixed indenting, updated version number