+1
incognito
Can TO open a saved window as incognito. I have several ebay accounts, but when i restore the previously saved incognito windows, they are no longer incognito and so i can only use on eaccount
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Supporting incognito mode is not a small problem unfortunately. And this is further complicated by Chrome bugs in Incognito mode for extensions API.
This is big work and not something in a high priority. So i will not promise you quick fix for this.
(And actually It is a bad idea to enable extensions in Incognito, they are disabled in incognito mode for a reason)
The only thing i can advise you as a workaround is to create separate profile in Chrome, specially for your incognito activities where you want to track something using the TO. And install the separate TO instance in this profile. Then you will be able to clear this profile data (the cookies, the history, and thing like this) separately from your main Chrome profile.
A MUCH better solution is to just disable back the TabsOutliner in Incognito mode (as it is by default), and do not use it for managing your incognito windows.
I think you have only few of them anyway and unlikely they need to be managed in TO as they most likely have very special purpose. In other cases using the separate profile for such activities have much more sense.