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Remove out-of-date source code links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.
Merge pull request #1366 from ctrueden/devel/cleanup

Miscellaneous cleanup