FYI, the user guide documentation says that the existing synonyms.txt file can be found at:
Integrated Genome Browswer / core / igb / scr / main / resources / synonyms.txt

But in fact the file is located here (path on bitbucket):
Integrated Genome Browser / core / synonym-lookup / src / main / resources / synonyms.txt

and here (additional path on my machine, not available on bitbucket):
Integrated Genome Browser / core / synonym-lookup / target / classes / synonyms.txt

The outdated user guide page is here:
https://wiki.transvar.org/display/igbman/Use+synonyms.txt+to+link+genome+version+names+to+each+other

Users are directed to look at the current file before making changes, and using the current file as an example is the only way we tell users how to format their synonyms file.

*update*
I have created an issue about this
IGBF-1229
file location of synonyms.txt in user guide

When IGB saves the synonyms info, the files in the file paths I showed above do not change.
The following is added to preferences:

<key>data directory</key>
<string>/Users/ivory/Downloads/synonyms.txt</string>
...
<key>locations/</key>
<dict>
<key>Version Synonyms File URL</key>
<string>/Users/ivory/Downloads/synonyms.txt</string>
</dict>

When IGB starts (after reseting preferences) the locations node is empty and the data directory node does not exist.

After selecting a genome and then selecting the synonyms file, the data directory node is created and populated with the file name, but the locations node is still empty.
Choosing to close IGB (in the pop up window) does not change this. Opening IGB does not change this.

From the home screen, after selecting the synonyms file, the data directory node is created and populated with the file name, and the locations node populated with the file name.

Whatever is called to populate the locations node is being called when IGB is on the home screen
but not when IGB is in a genome, and not when the program is closed for this purpose.

The key line for this is in the file SynonymsControPanel.java
line 131
PreferenceUtils.getLocationsNode().put(PREF_VSYN_FILE_URL, vsynonymFile.getText());

There is a very similar line for the chromosome file, in fact the block of code this lives in is pretty much identical.

When IGB prompts the user to restart, this code hasn't run yet. If the user opts to quit IGB, then the program quits without ever saving the update to the locations node.
The code block needs to catch the file=="" case (where the user has removed the synonyms file) and the file-selected case. Since these two cases are separated in the logic flow, the code has to be in two different places. So I pulled relevant code into a method (called updateSynonymFile) that applies to both the genome version synonyms and the chromosome synonyms. In addition to replacing the existing code blocks, I added a call to this function in the file-selected case logic.

Testing results are the same as my last comment EXCEPT that if the genome version is selected, and the I choose a synonym file, the locations node is updated immediately (before I choose to quit or not). When I choose to quit and then re-open IGB, my updated synonyms file is preserved between the sessions.

Since the IGBF-1187 branch has already been merged into master, I made a new branch IGBF-1187-b for these updates.
See
https://bitbucket.org/IvoryBlak/integrated-genome-browser/branch/IGBF-1187-b

Since Mason was the one who identified the problem, I think he should be one of the first level reviewers to make sure it is resolved.
I'm moving this to needs first level review.

Labeling as Intermediate due to past workflow confusion. Not clear if this is fixed or not.