Merge pull request #486 from mtbc/rebased/develop/warn-data-loss

put permissions warning into a proper warning box (rebased onto develop)
fix variable name for consistency
Merge pull request #2 from mtbc/fix-code-examples

in Java code example fix variable name for consistency
Merge pull request #487 from joshmoore/rebased/develop/fix-code-examples

Fix Java code examples (rebased onto develop)
merge develop -D org -I include -E exclude: PR 450 (omero: Python 2.6 is the minimum supported version)