Done (Includes Dr.Freese's work as well):
Plugin - Graph thresholding visual analytics
Plugin - Track Operations API, GUI
Plugin - App Manager GUI
Plugin - Save Image GUI
Plugin - Save Session Manager
Plugin - Advanced Search Tab
Plugin - Selection Info tab
Plugin - Graph Tab
Plugin - Selection Info tab
Plugin - BAM data format handler
Plugin - Restriction Sites tab
Plugin - Bigbed data format handler
Plugin - Bigwig data format handler
Plugin - Annotation Tab
Plugin - App Store REST API
Plugin - BAI index visualization handler
Plugin - Console Tab
Plugin - Sorting API and Impl
Plugin - BED file format handler
Plugin - Feedback
Plugin - Bookmarks and REST API
Plugin - Data caching GUI
Plugin - Toolbar Preferences GUI
Plugin - Keyword Search
Plugin - Data caching API
Plugin - External View
Plugin - Sequence Viewer GUI
Plugin - File Handler - Genotyping Results
Plugin - Script handler
Plugin - Paired-end Read Preprocessor
Plugin - Search Id or Props

Moving to first level review.
pull this branch in order to test.

Tested on Mac.

Everything is working as expected.

Regarding the commits, please revert 0945a70 (This is a combination of 2 commits) and recommit the changes for the two plugins separately. Then create a pull request to main-JDK8-r6.

Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/941

Installers are built and ready for testing. See: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

Tested Mac Installer.

IGB started with no errors in log. Behavior was normal, able to load all plugins (did not try MI bundle which has its own ticket).

Closing ticket.