Somehow clicking a link in console started to open the corresponding file in a separate window not in the current editor window. I found that it's due to similar file existing in the source directory. Sometime ago I had BitTorrent Sync (https://getsync.com/) installed, and enabled syncing the source directory. It turns out that clicking the links revealed the files from (hidden) .sync subdirectory that contained copies of the source files. Removing that directory resolved the problem.
Somehow clicking a link in console started to open the corresponding file in a separate window not in the current editor window. I found that it's due to similar file existing in the source directory. Sometime ago I had BitTorrent Sync (https://getsync.com/) installed, and enabled syncing the source directory. It turns out that clicking the links revealed the files from (hidden) .sync subdirectory that contained copies of the source files. Removing that directory resolved the problem.