What has 'rm -r ~' done to my home directory?

You have deleted (almost) all of your home directory!

rm -r something recursively deletes files and directories in/under something; it will only fail on items it does not have permission to delete, either because they are owned by a different user (e.g. root), or because they are in use (e.g. a GVFS mount).

If you did not add -f (as in, rm -rf something), you would get something like:

rm: remove write-protected regular file ‘something’?
rm: descend into write-protected directory ‘something’?

At this point you can abort and you then likely realise that you executed the wrong command.

Suggestions from the community on how to avoid such accidents

Note: Community wiki, everyone please feel free to contribute.

• For a few files, use the -i option to get a confirmation on removing files or directories:

  $ rm -ri something/
  rm: remove regular file ‘something/file~’? y
  rm: descend into directory ‘something’? y
  rm: remove regular file ‘something/file’? y
  rm: remove directory ‘something’? y
  

• If removing from a current directory, prefix it by a ./ to avoid mistakingly removing a different location.:

  $ cd something
  $ rm -v ./*~
  removed ‘./file~’
  

  The above was for demonstrating the use of ./. If there is a subdirectory, you can of course use rm -v something/*~ as well. Beware: do not think that rm ./.* removes all hidden files in the current directory. See this Serverfault question for workarounds on hidden files globbing.

• Move rather than delete: Rather than deleting files recursively in the first place I got used to move the files I want to get rid of somewhere else before I delete them finally. If something went wrong its easy to restore.

  mv -b SOURCE DEST
  

• Use find (possibly with grep) to preview if you want to recursively delete selected files. You should try to make this a rare occurrence, but if you have to...

  1. find with no arguments recursively lists all files/directories under the current one. You should try to look up man find on how to make it selective (a treasure trove), but if you don't want to bother, you can just use the familiar grep to filter for the files you want to delete.
  2. Suppose I'm an uber-l33t kernel hacker, and am bothered by the few KBs of "example" files in my source tree; I want to delete all files containing that in the name. So I type find | grep example, which gives me these 20 files. That looks good, so I now go and delete those exact files, along with the rm -v verbose output previously mentioned, via xargs:

     find | grep example | xargs rm -v

     which gives me this output. Such previewing prevents problems where say, you make a typo and type sample instead of example.

The above solution should not be used if you may have filenames containing spaces, tab characters, newlines, or quotes (" or '), as this will lead xargs to either fail, or feed rm with incomplete filenames, which in worst case could end up removing the wrong files. The safe way to do the above is to do it all with find's operators and actions.

The following will show all files that contain the word example

find . -name "*example*"  

If that list is the files you want to remove, use the -exec action to pass the files to rm.

find . -name "*example*" -exec rm -v {} +

See Using Find for more help with using find.

Yes. An unquoted tilde character as a separate argument gets expanded to your homedir. So rm -r ~ got expanded to rm -r /home/yourusename. So you told rm to recursively delete all files in your homedir.

See http://www.gnu.org/software/bash/manual/bashref.html#Tilde-Expansion for more about how tilde expansion works.