Add sifting appender to split logfile by thread

With this commit, the log for each thread in multi-threaded automated tests
should be stored in its own logfile simplifying the result parsing. The thread
is removed from the appender pattern to prevent duplication.
Add debug level info to the logfile

This should ideally simplify detection of errors
Log unsuccessful metadata result using the ERROR debug level
Increase SiftingAppender timeout to 60 minutes
Move automated tests log files to target/ directory
Clean target/ directory as part of the `clean` target of build.xml
Fix whitespace with ERROR debug level
Fix logback configuration to pass loci.tests.testng INFO to stdout only

The logfiles created with the SIFT appender should still contain the FormatReader INFO and the loci.tests.testng DEBUG level.
Move additional logging at DEBUG level to strip it from console output
Set parseConfigFile() exception output at DEBUG level
Replace deprecated layout sub-component by encoder
Deprecate TestTools.createLogFile()
Explicitly set the encoder class to PatternLayoutEncoder
Merge pull request #1117 from rleigh-dundee/cpp-doxygen

cpp: Minor doxygen fixes
Merge pull request #1121 from sbesson/rebased/develop/bfgetplane_fix

Fix bfGetPlane tile input check (rebased onto develop)
Update auto-generated documentation

Repository: openmicroscopy/bioformats
Already up-to-date.

Generated by BIOFORMATS-5.1-latest-docs-autogen#63 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.1-latest-docs-autogen/63/)
merge develop -D org: PR 857 (Initial support for Zeiss .lms files)
merge develop -D org: PR 858 (Initial support for Veeco AFM data)
merge develop -D org: PR 981 (Ignore namespaces when filling in an XMLAnnotation's Value)
merge develop -D org: PR 983 (Woolz: make sure the service is initialized when calling openBytes (rebased onto develop))