declaring plugins in the JBrowse trackList.json and the Apollo should not disable plugins

[nathandunn]

In reference to this:

http://gmod.827538.n3.nabble.com/elastic-search-in-genome-apollo-tp4059909p4060113.html

We either need to remove plugins from the jbrowse trackList.json (to be re-added by Apollo) or just guarantee they do not collide

[cmdcolin]

This is potentially something jbrowse should check for on its side of things. A bug exists for it here GMOD/jbrowse#897

[nathandunn]

Yeah, this is a tricky issue. Ultimately Apollo is reading in the trackList.json and "faking it" when it comes in, so we might be able to fix it for our use-case of users re-using the same directory or config files. . . . I'll watch it if you get anywhere on it. We still have to get to 1.16 if we can.

[nathandunn]

This has already been worked around on another bug.

[nathandunn]

The other issue was this: https://github.com/GMOD/Apollo/pull/2007/files#diff-2fd45819f7cf7c70bbdc718d5b19faefR465

But the reason for the fix was this: #2007 (comment)