I've patched the ackmate plugin for textmate to fix the problem described in this issue:
Searching inside symlinked folders opens a new window http://github.com/protocool/AckMate/issues#issue/5
Trevor Squires had been opening a a file like this from the plugin:
[[[NSApplication sharedApplication] delegate] openFiles:[NSArray arrayWithObject:absolute]];
Evidently after passing through Cocoa the original path to the file, which includes a dir symlink, is converted to the equivalent path without the symlink before textmate proper gets the event. Texmate then opens the file in a new window because it isn't in the project path anymore.
Here's the change I made: http://github.com/stepheneb/AckMate/commit/1bc7e4ca698b51b2a0d523ecea277bfb8...
Which was to call Texmate going through the shell with an NSTask.
I'm wondering if there is a better way -- Trevor thought my hack was a bit ugly ;-)