Add slf4j-log4j dependency in the test-suite component

This should fix a bunch of test failures.
Add slf4j-log4j to the test classpaths

This allows the tests to pass without requiring slf4j-log4j across the
board.
Fix slf4j-log4j artifact ID
Fix POMs to include slf4j-log4j and log4j as test dependencies
Remove slf4j warnings
Fix source code links moved to the scifio-tools foder
Remove slf4j warning about multiple implementations

When a runtime classpath contains a built jar under
${artifacts.dir} it's not necessary and in fact confusing
to include slf4j-log4j12 on the classpath.
Remove log4j. warnings on missing log4j.properties
Remove duplicate Maven dependencies
Add log4j.properties to all testng classpaths

As in 916e4532c4c5, add the tools directory to the classpath
for testng execution so that log4j.properties can be found.

Also perform some minor cleanups.
Remove slf4j-log4j12 from all components

As in 5fea921a33ea0, remove slf4j-log4j12 from the runtime
classpath properties to prevent warnings about multiple
implementations.
Remove hard dependency on log4j

Conflicts:
	components/autogen/pom.xml
	components/metakit/build.properties
	components/ome-xml/pom.xml
Add ../../tools to surefire maven plugin classpath
Add surefire with classpath fix to loci-plugins
Move to ant/log4j.properties at WARN

The log output was 4MB+ which caused travis
to error out. Reducing this my having a second
test-only log4j.properties file.
Remove loci.formats.utests.tiff.OMETiffWriterTest

All this test does is check for open file handles; we now have much more
comprehensive tests that cover the same thing (and without depending
upon log4j).

Conflicts:
	components/scifio/test/loci/formats/utests/tiff/OMETiffWriterTest.java
Remove commented-out log4j code from the ome-io component

These classes are beyond obsolete anyway, and will likely be removed in
the next major release.
Merge pull request #390 from joshmoore/rebased/develop/slf4j-fixes

Add slf4j-log4j dependency in the test-suite component (rebased onto develop)
Merge pull request #392 from melissalinkert/logging-docfix

Logging docfix (rebased onto develop)