Rosetta started life as a small project in the lab of David Baker at the University of Washington. It was written in FORTRAN and focused on ab initio structure prediction of small proteins.
Over the years the capabilities of Rosetta were extended to do things such as design and small molecule docking. To allow for better extension of capabilities, Rosetta was translated to C++. This was released as Rosetta2 or Rosetta++.
Despite this success, the structure of the code from the early FORTRAN days was limiting further development. A project to rewrite Rosetta using good object-oriented practice was launched. This cleaned up code was released as Rosetta3 (aka "minirosetta" or "mini"). Rosetta3 allowed extension of Rosetta into PyRosetta, FoldIt, RosettaScripts, ROSIE and more.
Note: Over the years Rosetta versioning nomenclature has changed. Rosetta has transitioned from no versioning, to CVS, to SVN, to git/GitHub. One of the more stable versioning methods is derived from the SVN years, which has been extended into the git years. These numbers are listed below starting with 'r', and denote either SVN revisions, or git merges to the master branch numbered continuously with SVN.
Late 2006 to Early 2007