I think since 1.6 (I'm at 22.214.171.124) "Re-open project windows at startup" stopped working.
I have project(s) open quit Source tree, start it again and I only get Bookmarks window.
This worked nicely before 1.6 versions.
One possible reason I can think of I completely disabled OS X automatic application state saving (it was disabled even before 1.6 updates) and Source Tree begun relying on it and wasn't before.
There's an option in your system preferences on your Mac that controls this. They're named differently and are reversed between OS X versions as follows:
If you could try that setting out and see if it resolves your problem. If not, we can come back to it and re-address the issue.
Then why is there option in Source Tree when it depends on OS to do that?
The most annoying new feature of OS X is that restore windows, which I disabled (i.e. forbid access to "~/Library/Saved Application State" folder ).
And before 1.6 version of Source Tree it worked well, and since 1.6 is the first app that I have where I miss function.
using stree in project folder from terminal opens project window, but still Bookmarks window pops up along it, which is kinda annoying but at least is a semi workaround.
This is because we now honour the OS preferences from 10.7 onwards. There's a system preference because 10.6 needs support for it.
I've filed an issue to get rid of the SourceTree preference for 10.7+ here: https://jira.atlassian.com/browse/SRCTREE-1642
Hope that helps
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