Merging the two repos – Kathleen’s Lab Notebook

I currently have two repos containing code and data relevant to the ceasmallr project: The ceasmallr repo, which Steven originally created and which contains Sam’s data preprocessing work (e.g., Bismark), and my kathleen-coral repo, which I created to work on the ceasmallr data as part of Steven’s FISH 546 class project. Ultimately, though, it is most appropriate to have all of the ceasmallr relevant work to be contained within the ceasmallr repo. I’ve forked the ceasmallr repo so that I have a self-owned version to continue working in. I now need to figure out how to accurately merge the two repos in a way that is both functional and accurately documented in the git history.

RESULT

All ceasmallr relevant work now available, and will be continued from, my fork of Steven’s ceasmallr repo: github.com/shedurkin/ceasmallr

Merging

To help with this, I’m using Claude Opus 4.8.

Prompt: >I have two github repos that both contain work for a single project. One, ceasmallr contains work through the data preprocessing, while the other, kathleen-coral contains analysis work. I want all of the analysis work to also be included in the ceasmallr repo, and to continue the rest of the work from that repo. What is the easiest and most sound way to do that? Ideally the solution would be clealry documented in the git history. > >Technically I only want to merge the project directory of kathleen-coral with ceasmallr. Both ceasmallr and kathleen-coral/project have the same high-level structure (files contained within the primary directories of data, code, or output), and I’d like the structure to be maintained (i.e., code files from the analysis repo are placed in the code directory of the OG repo)

Make a disposable clone to operate on (protects the original):

bash
cd ..
git clone kathleen-coral kc-split
cd kc-split

Extract project/ to the root, rewriting history:

bash
git filter-branch --prune-empty --subdirectory-filter project HEAD

Merge into ceasmallr on an integration branch:

bash
cd ../ceasmallr
git status                    # clean
git checkout main             # or master
git checkout -b merge-analysis

git remote add kc ../kc-split
git fetch kc
git branch -r | grep kc       # confirm the branch name (main vs master)

git merge --allow-unrelated-histories kc/main \
  -m "Merge analysis work from kathleen-coral/project

Imports the full commit history of the analysis work (previously the project/ directory of the kathleen-coral repo). Its code/, data/, and output/ trees merge into the existing top-level directories here. Future analysis continues from this repo.”

(Swap kc/main for kc/master if that’s what step 3’s grep shows.)

Resolve collisions, if any. Files under code/, data/, output/ merge cleanly as long as filenames don’t overlap. The usual conflicts are shared top-level files (README.md, .gitignore, LICENSE, a .Rproj) as add/add conflicts — open each, combine, then:

bash
git add <resolved-file>
git commit                    # completes the merge commit

Verify the history came across:

bash
git log --oneline --graph --decorate | head -40
git log --oneline -- code/
git log --follow -- code/<some-analysis-file>.R

Finalize and clean up:

bash
git remote remove kc
git checkout main
git merge --no-ff merge-analysis
cd ../ && rm -rf kc-split      # disposable clone, no longer needed
cd ceasmallr
git push