When I merge master down into my dev branch, EGit shows files in conflict. So I go to the Git Staging view, where the conflicting files are shown under "Unstaged Changes" with a red conflict marker on their name. For each file, I right-click it, choose "Merge Tools", the conflict editor shows up with my code on the left and the master code on the right, I manually solve the conflicts and add the file to the index, so it moves from "Unstaged Changes" area to "Staged Changes". This is all good.
However, when I open the Merge Tool, while the editor actually displays the non-conflicting changes in blue and the conflicting changes in red, in many occasions there are no red changes at all, only blue changes, as though there were no conflicting changes whatsoever, and all I do to solve the conflicts (?) is to click "Copy all non-conflicting changes from right to left".
So why was the file shown as conflicting in the first place ? There must be something going on that I am missing big time. This is what I'm trying to understand.
ADDED: While my main reason for concern is simply that I don't understand why there are no changes marked in red in a conflicted file, so I'm not sure what's going on, so I might be screwing up when committing back to master, another big point of this issue for me is that all those files marked as conflicting but showing no conflicting changes are dealt with by simply copying the non-conflicting changes (that is all the changes) from right to left, which to me amounts to making my file identical to the one being merged into mine, which in turn would amount to simply overwriting my file with the other one, which is something that I think I shouldn't be doing manually file by file. So I'm also trying to understand if there is a way to make the EGit merge automatically replace my files when they are in that state (that is in conflict but with no conflicting changes marked).