Add missing EOF newlines

This was accomplished using:

git ls-files \*.java | xargs sed -i '' -e '$a\'
Remove out-of-date source code links

This was performed using these tricks:

git ls-files \*.java | xargs sed -i '' -e '/\>Gitweb\</d'
git ls-files \*.java | xargs sed -i '' -e '/\>Trac\</d'
git ls-files \*.java | xargs sed -i '' -e '/\<dl\>\<dt\>\<b\>Source/d'
git ls-files \*.java | xargs sed -i '' -E -e '/^ \*$/ {N; s/^ \*\n( \*\/?$)/\1/; }'

Since the source files no longer have source links embedded,
this commit also removes the Perl source link checker script.

Edit: This commit actually does not remove the source links anymore,
since they were already removed in the meantime; see:

    https://github.com/openmicroscopy/bioformats/pull/1455

But the rebased commit is preserved here so the relevant sed commands
are still documented, in case something similar needs to be done in the
future.
Extend copyright year range to 2014

It was done with the following shell command:

    git grep -l 'Copyright (C) [0-9]\{4\} - [0-9]\{4\}' | \
    xargs sed -i '' -e \
    's/\(Copyright (C) [0-9]\{4\} - \)[0-9]\{4\}/\12014/'

The license-maven-plugin would normally do it for us. Unfortunately, it
cannot, because we have the canUpdateCopyright flag set to false, so the
update-file-header goal cannot update the copyright year range on files
with existing headers. The flag must be false because otherwise, it
would overwrite each file's copyright holders (we have a few files with
non-default copyright holders listed, which we want to preserve).

In the future, we could address the issue by contributing an enhancement
to license-maven-plugin that splits canUpdateCopyright into two parts:
canUpdateCopyrightYears and canUpdateCopyrightAuthors.
Add missing @Override annotations
Remove tabs from files indented with spaces

This was done manually, but with the help of vim's ":retab" command.
Add test checking that the reader used is the OME-TIFF reader.
Merge pull request #1366 from ctrueden/devel/cleanup

Miscellaneous cleanup
Merge pull request #1454 from rleigh-dundee/cpp-metadata2

C++: Autoload schema catalogues and set up environment for tests
Merge pull request #1456 from mtbc/eclipse-import

add note about using mvn eclipse:eclipse
Merge remote-tracking branch 'origin/develop' into im3

Conflicts:
	components/formats-bsd/src/loci/formats/in/IM3Reader.java
Add doc.
Prevent potential NPEs when close() is called
merge develop -Dorg -Ssuccess-only: PR 1365 (PrairieView 5.2 fixes and improvements)
merge develop -Dorg -Ssuccess-only: PR 1407 (TIFF: fix plane count calculation for pyramids with multiple planes)
merge develop -Dorg -Ssuccess-only: PR 1420 (Updating samples and adding units samples)
merge develop -Dorg -Ssuccess-only: PR 1437 (Changed handling of empty series names in ND2 files)
merge develop -Dorg -Ssuccess-only: PR 1442 (Update roi handler)
merge develop -Dorg -Ssuccess-only: PR 1457 (IM3: fix memoization and whitespace)
merge develop -Dorg -Ssuccess-only: PR 1459 (Fix writing of tiff description)
merge develop -Dorg -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1458 sbesson 'Fix Javadocs warnings' (label: exclude)
  # PR 1460 rleigh-dundee 'C++: Implement MetadataConverter' (status: pending)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1426 qidane 'Initial Rendering Definitions schema' (exclude comment)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1461 csachs 'Changed ND2 metadata string handling to work properly with empty strings' (user: csachs)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1381 melissalinkert 'Parse physical pixel sizes from CellSens .vsi datasets' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1443 joshmoore 'Genshi ZIP' (label: exclude)
Updating ac6a0ab..237d975
Previously merged:
  # PR 1456 mtbc 'add note about using mvn eclipse:eclipse'
  # PR 1454 rleigh-dundee 'C++: Autoload schema catalogues and set up environment for tests'
  # PR 1366 ctrueden 'Miscellaneous cleanup'

Merged PRs:
  # PR 1365 ctrueden 'PrairieView 5.2 fixes and improvements'
  # PR 1407 melissalinkert 'TIFF: fix plane count calculation for pyramids with multiple planes'
  # PR 1420 qidane 'Updating samples and adding units samples'
  # PR 1437 stelfrich 'Changed handling of empty series names in ND2 files'
  # PR 1442 bramalingam 'Update roi handler'
  # PR 1457 melissalinkert 'IM3: fix memoization and whitespace'
  # PR 1459 jburel 'Fix writing of tiff description'

Generated by OME-5.1-merge-push#628 (http://ci.openmicroscopy.org/job/OME-5.1-merge-push/628/)