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I was trying to merge a dev branch into master. git checkout master git pull . dev Everything seemed to go well, although there were conflicts I fixed these and commited. But when I checked this newly merged working tree is missing a lot of folders and files from dev. git status // Shows conflicts & doesn't list some files/folders. git commit -a Created commit 55ffdd1: Merge branch 'dev' into master git diff dev --name-status Produces: D folders/lm.gif D folders/lmh.gif ... So the files/folders that didn't show up on 'git status'. It also didn't show up at the end when I fixed the merged conflicts. Also when I try to merge again it says: git merge dev Already up-to-date. Yet the master branch clearly is missing files/folders from the dev branch. Why is that? Shouldn't that folder and all it's contents be added? 'folders' is being tracked on the dev branch, so shouldn't it have gotten pulled over when I did the merge? When there was a merge conflict earlier did git stop the merge process and skipped a bunch of files/folders? The dev branch had quite a lot of changes, could I have messed something up with git in the past that now certain files/folders wouldn't have merged? (When I first created the dev branch I didn't know what I was doing and did crazy things like reset, reverts etc.) Hoping one of you git guru's here on stack overflow knows the answer. :) Thanks, Quang Answer Thanks Walter, Yes this is what happened. After doing some investigating I found out it was a little complicated what happened. It turned out that. dev branched from master, it had all the files. A third branch, lets call it "cleaned", branched off of dev. cleaned branch deleted all the files. cleaned b

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