CellomicsReader: Improve performance of initFile

Move checking for hidden files to inside the loop over the file list.
This avoids creating a Location object for each file twice: inside
the loop and in Location.list().
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 pull request #507 from rleigh-dundee/cellomics-location-perf

CellomicsReader: Improve performance of initFile
Merge pull request #514 from melissalinkert/file-handle-cleanup-stable

Prevent false positives in open file handle test (rebased onto dev_4_4)