I enjoy using source tree but sometime when Im using it I like to do some commands (like merge, creating branched) from the terminal. Can doing this cause me any problems whatsoever? Thank you!
You can do this safely. whenever one of them is changing something, it creates a lock that prevents the other one from changing things.
See here for experiences using git-GUIs/git commandline in parallel. My experience says, that there shouldn't occur any problems (at least I hadn't any yet). The only annoyance might be, that GUI-Tools might need some refresh after performing some git actions outside the GUI
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