Improve bfCheckJavaPath performance testing

This commit should fix instabilites in the daily build of TestCheckJavaPath.
Successive calls to bfCheckJavaPath are not treated as independent. More
precisely, performance is only assessed for the third call and onwards.
Fuji: make carriage returns optional
Merge pull request #768 from sbesson/rebased/dev_4_4/matlab_performance_test

Improve bfCheckJavaPath performance testing (rebased onto dev_4_4)
Fix link to Homebrew Github repository
Merge pull request #779 from sbesson/rebased/dev_4_4/homebrew_link

Fix link to Homebrew Github repository (rebased onto dev_4_4)
Merge pull request #776 from melissalinkert/fuji-line-endings

Fuji: make carriage returns optional