Projects evolve, code boundaries change. Git commit history shall be preserved.

Split Repo
Split files out into a new repo preserving all history. Existing repository: perl. File to preserve:

First, clone the existing repository to a new location, as it will be carved down to just the file(s) we need, thereby becoming the new desired repository:

cd tmp
git clone ~/workspace/perl
cd perl
git remote remove origin

Remove everything but the matching file by use of filter-branch. There are other approaches, particularly for subdirectories, but I found this to work best (all one line):

git filter-branch -f --prune-empty 
     --index-filter 'git ls-tree -z --name-only --full-tree HEAD | 
     grep -zv "^$" | 
     xargs -0 git rm --cached -r -f --ignore-unmatch' -- --all

Rebase to eliminate commits related to renames that are not related to this file, and only remain because git ls-tree did not find these non-existent files for our filter:

git rebase --onto bf1fbad2b6f766b80c2a07edacd7084c6d3fd252 e490b6cb41ca541b7e468148a62f63435366836f
git rebase --onto 31fe475fe0c7314a2f307fa1c201cd2f9eca6992 bf1fbad2b6f766b80c2a07edacd7084c6d3fd252

Garbage collection on 694 objects at 4MB:

git gc
Counting objects: 694, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (674/674), done.
Writing objects: 100% (694/694), done.
Total 694 (delta 253), reused 0 (delta 0)

du -csh .git/objects/
592K	.git/objects/
592K	total

Merge Repos
Merge several repositories, each into subdirectories of a new repository, preserving all history. New repository: unix. Project to merge: ccli.

First, clone the project we wish to merge in so as to preserve the original in case something goes awry:

cd tmp
git clone ~/workspace/ccli
cd ccli
git remote remove origin
cd ..

Now back at top-level tmp, create a new target repository and start with a an initial dummy commit

git init unix
cd unix
echo "initial" > deleteme.txt
git add deleteme.txt
git commit -m "Initial commit."
git rm ./deleteme.txt
git commit -m "Initial delete."

Add a remote to the ccli repo:

git remote add ccli ../ccli
git fetch ccli
git merge ccli/master

Move files and commit:

mkdir ccli
for i in $(ls -1 | grep -v ccli); do git mv $i ccli; done
git mv .ccli_env_example ccli
git commit -m "Move ccli project into ccli subdir"
git remote remove ccli

Repeat for each project to merge in.

NOTE: Alternative is to fetch each project into separate branches, merge the branches. Cleaner, but end result same.
NOTE: Requires –follow flag to track full file history in git log, as this is a move like any other. There may be a history rewrite alternative.
NOTE: Approaches with submodules keep subdir distinct so future changes from upstream can be brought in. This is not what we want, as we wish to glue things together permanently.

Should we desire to share our work by pushing it to a new remote repository, such as GitHub:

git remote add origin
git push -u origin master