Figured it out, but not obvious: In files pane, right-click "Source Control..." -> "Clear login information". Restart MATLAB, then "Manage Files..." is clickable, and I can select the new repository path.
How to fix "Could Not Get Repository Location" when "Manage files..." is greyed out?
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SVN worked for a while, then our server configuration changed somehow. Now, when trying to add a file to SVN, I get an error dialog with "Repository: Could Not Get Repository Location". Right-clicking in the file area, "Source Control..." shows "Manage Files..." greyed out. MATLAB (8.4.0 2014b) Bulit-In SVN Integration (1.8) Using Tortise SVN.
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