Merge pull request #509 from melissalinkert/e283fb8e38042f5b0da2578e7c7fb07f838b92ca

ScanR: clear the pixel buffer when an invalid TIFF is found
Merge pull request #511 from rleigh-dundee/deprecate-abstractomexml-methods

AbstractOMEXMLMetadata: Deprecate methods removed on develop
Prevent false positives in open file handle test

Noticed by Jenkins when using Java 1.5.

Conflicts:

	components/test-suite/src/loci/tests/testng/FileHandleTest.java
merge dev_4_4 -D org -I include -E exclude: PR 507 (CellomicsReader: Improve performance of initFile)
merge dev_4_4 -D org -I include -E exclude: PR 514 (Prevent false positives in open file handle test (rebased onto dev_4_4))