Trackster: resize viewport when showing reference track to avoid inadvertently hiding scroll bar.
Trackster: remove mousewheel scrolling amplifier and clarify comment.
Allow tool conf 'tool_path' resolution relative to conf file.
Relative 'tool_path' directories are resolved relative to GALAXY_ROOT (or really working directory). This is probably the expected behavior - but I think it is advantageous to be able to find tools relative to the tool_conf file also. This can now be done using string.Template resolution of ${tool_conf_dir}.
Make galaxy.util.in_directory slightly more generic to match Pulsar's variant.
Fixes failing unit test in just added code.
Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.
Charts plugin update
Charts style update
Merge
Style fix: use Safari/webkit specific syntax for flexbox to correct layout of paired-collection-creator in Safari
Style fix: use MS/IE specific syntax for flexbox to correct layout of paired-collection-creator in IE10 (Note: IE9 has no flexbox and this interface can't be used with it)
Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests
Merged in jmchilton/galaxy-central-fork-1 (pull request #423)

Allow tool conf `tool_path` resolution relative to conf file.
Add documentation about local runner destination option embed_metadata_in_job.
Merge.
Another docfix for recent local job runner changes.
Enhance the tool shed repository API controller to allow filtering by owner's username or repository name.
Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon).
Pack script.
Merged in jgoecks/galaxy-central-gcc-2014-fixes/stable (pull request #425)

Trackster fixes
Updated tag latest_2014.06.02 for changeset 8a863a311a6c