Combining multiple git repositories

phd/code/
phd/figures/
phd/thesis/

cd phd/code
git commit
cd ../figures
git commit

cd phd
git commit

cd phd
git init
git add [[everything that's already in my other repositories]]

$ cp -r phd phd-backup

$ cd phd/code
$ git filter-branch --index-filter
    'git ls-files -s | sed "s-t-&code/-" |
     GIT_INDEX_FILE=$GIT_INDEX_FILE.new
     git update-index --index-info &&
     mv $GIT_INDEX_FILE.new $GIT_INDEX_FILE' HEAD

phd
  |_code
  |    |_.git
  |    |_code
  |         |_(your code...)
  |_figures
  |    |_.git
  |    |_figures
  |         |_(your figures...)
  |_thesis
       |_.git
       |_thesis
            |_(your thesis...)

$ cd phd
$ git init


$ git pull code
$ rm -rf code/code
$ rm -rf code/.git


$ git pull figures
$ rm -rf figures/figures
$ rm -rf figures/.git


$ git pull thesis
$ rm -rf thesis/thesis
$ rm -rf thesis/.git

phd
  |_.git
  |_code
  |    |_(your code...)
  |_figures
  |    |_(your figures...)
  |_thesis
       |_(your thesis...)

$ cd phd/code
$ git mv code code-repository-migration
$ git commit -m "preparing the code directory for migration"

$ cd phd
$ git mv code/code-repository-migration code/code
$ git commit -m "final step for code directory migration"

$ cd phd/code
$ mkdir code
# This won't work literally, because * would also match the new code/ subdir, but you understand what I mean:
$ git mv * code/
$ git commit -m "preparing the code directory for migration"

$ cd ../..
$ mkdir phd.all
$ cd phd.all
$ git init
$ git pull ../phd/code
...

git init
git add *
git commit -a -m "import everything"

Rewrite 422a38a0e9d2c61098b98e6c56213ac83b7bacc2 (1/42)mv: cannot stat `/home/.../wikis/nodows/.git-rewrite/t/../index.new': No such file or directory