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docs: add Git LFS prerequisite and SkillKit cross-agent section#110

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docs: add Git LFS prerequisite and SkillKit cross-agent section#110
Gonzih wants to merge 1 commit into
K-Dense-AI:mainfrom
Gonzih:docs/git-lfs-prereq-and-skillkit

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@Gonzih

@Gonzih Gonzih commented Mar 26, 2026

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Closes #106, closes #47

Summary

  • Git LFS prerequisite (Suggestion: Add Git LFS to Prerequisites in README? #106): Add brew install git-lfs && git lfs install (and Linux/Windows equivalents) to the Prerequisites section so new users don't hit checkout failures when cloning large skill assets tracked with Git LFS
  • SkillKit cross-agent section (Add SkillKit commands for cross-agent compatibility #47): Add a "Use with Other AI Agents (via SkillKit)" section near the bottom of README.md showing how Cursor, Codex, Gemini CLI, and Windsurf users can use skillkit to search, install, and translate skills without manually copying folders
  • Update Table of Contents to link the new SkillKit section

Test plan

  • Verify Prerequisites section now includes Git LFS installation for macOS, Linux, and Windows
  • Verify "Use with Other AI Agents (via SkillKit)" section appears before Citation section
  • Verify Table of Contents links resolve correctly

- Add Git LFS installation instructions to Prerequisites (closes K-Dense-AI#106)
  so new users don't hit checkout failures with large skill assets
- Add 'Use with Other AI Agents (via SkillKit)' section (closes K-Dense-AI#47)
  documenting SkillKit for Cursor, Codex, Gemini CLI, Windsurf users
- Update Table of Contents with new SkillKit section link

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Comment thread README.md
git lfs install
```

After installing, re-clone or run `git lfs pull` in an existing clone to fetch the full file contents.

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FWIW uff, I didn't know that LFS is so ... annoying that it for some reason demands me to push something even if my PR is not modifying anything under LFS, and it seemed to do that until I fetched from that other remote (my fork) I had. So here might be needed

Suggested change
After installing, re-clone or run `git lfs pull` in an existing clone to fetch the full file contents.
After installing, re-clone or run `git lfs pull` in an existing clone to fetch the full file contents, and make sure you fetched your remotes before trying to push to avoid LFS attempting to push without necessity.

or alike.

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FTR here is the full protocol of the struggle just in case (I do not spot any secrets)
❯ git lfs checkout
Cannot checkout LFS objects, Git LFS is not installed.
❯ git lfs install
Updated Git hooks.
Git LFS initialized.
❯ git lfs checkout
Cannot checkout LFS objects, Git LFS is not installed.
❯ git push -u gh-yarikoptic enh-codespell
^Cloading LFS objects:   0% (0/1), 0 B | 0 B/s                                                                                                                                                                                    
Exiting because of "interrupt" signal.

❯ git push --help
❯ git push -u gh-yarikoptic enh-codespell
❯ git diff origin
❯ git remote -v
gh-yarikoptic	git@github.com:yarikoptic/claude-scientific-skills.git (fetch)
gh-yarikoptic	git@github.com:yarikoptic/claude-scientific-skills.git (push)
origin	https://github.com/K-Dense-AI/claude-scientific-skills (fetch) [blob:none]
origin	git@github.com:K-Dense-AI/claude-scientific-skills (push)
❯ git lfs pull
Skipping object checkout, Git LFS is not installed for this repository.
Consider installing it with 'git lfs install'.
❯ git lfs install
Updated Git hooks.
Git LFS initialized.
❯ git lfs pull
Skipping object checkout, Git LFS is not installed for this repository.
Consider installing it with 'git lfs install'.
❯ git diff gh-yarikoptic/main...
fatal: ambiguous argument 'gh-yarikoptic/main...': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
❯ git diff gh-yarikoptic/master...
fatal: ambiguous argument 'gh-yarikoptic/master...': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
❯ git br -a
* enh-codespell
  main
  remotes/origin/HEAD -> origin/main
  remotes/origin/main
  remotes/origin/orion/add-k-dense-web-gif
❯ git fetch gh-yarikoptic
From github.com:yarikoptic/claude-scientific-skills
 * [new branch]      main                      -> gh-yarikoptic/main
 * [new branch]      orion/add-k-dense-web-gif -> gh-yarikoptic/orion/add-k-dense-web-gif
❯ git diff gh-yarikoptic/main...
diff --git a/.codespellrc b/.codespellrc
new file mode 100644
index 0000000..bfd5625
--- /dev/null
+++ b/.codespellrc
@@ -0,0 +1,8 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git,.gitignore,.gitattributes,.codespellrc,*/scripts/office/schemas/*
+check-hidden = true
+# Ignore camelCase/PascalCase identifiers, bold-letter markdown/LaTeX, regex char classes, and URLs
+ignore-regex = \b[a-z]+[A-Z]\w*\b|\b[A-Z][a-z]+[A-Z]\w*\b|\*\*\w\*\*\w+|\\textbf\{\w\}\w+|\[\w+\]\w+|https?://\S+
+# Domain-specific terms: scientific abbreviations, tool/library names, medical terms
+ignore-words-list = simpy,som,ehr,hsa,braket,strat,infarction,caf,cafs,trough,mape,ket,fallow,ttest,cna,anc,fpr,namd,reacher,aer,ot,stard,commun,rouge,ois,als,blosum,recuse,theses,gage,coo,childs,ser,nd,inh,acn,toi,edn,whos,checkin,sortings,requestor,vermillion,pres,promis,abd,lod,varian,vor,bu,technik,gard,sav,magent,te,ontop,atomate,formate,slac,theis,sems,otu,scarches,whis,re-use
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
new file mode 100644
index 0000000..6e996fd
--- /dev/null
+++ b/.github/workflows/codespell.yml
@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@8f01853be192eb0f849a5c7d721450e7a467c579  # v2.2
diff --git a/scientific-skills/imaging-data-commons/SKILL.md b/scientific-skills/imaging-data-commons/SKILL.md
index 95fddaa..db18852 100644
--- a/scientific-skills/imaging-data-commons/SKILL.md
+++ b/scientific-skills/imaging-data-commons/SKILL.md
@@ -744,7 +744,7 @@ See `references/use_cases.md` for complete end-to-end workflow examples includin
 - **Estimate size first** - Check collection size before downloading - some collection sizes are in terabytes!
 - **Save manifests** - Always save query results with Series UIDs for reproducibility and data provenance
 - **Read documentation** - IDC data structure and metadata fields are documented at https://learn.canceridc.dev/
-- **Use IDC forum** - Search for questons/answers and ask your questions to the IDC maintainers and users at https://discourse.canceridc.dev/
+- **Use IDC forum** - Search for questions/answers and ask your questions to the IDC maintainers and users at https://discourse.canceridc.dev/
 
 ## Troubleshooting
 
❯ git diff --stat gh-yarikoptic/main...
 .codespellrc                                    |  8 ++++++++
 .github/workflows/codespell.yml                 | 23 +++++++++++++++++++++++
 scientific-skills/imaging-data-commons/SKILL.md |  2 +-
 3 files changed, 32 insertions(+), 1 deletion(-)
❯ git push -u gh-yarikoptic enh-codespell
Enumerating objects: 22, done.
Counting objects: 100% (22/22), done.
Delta compression using up to 20 threads
Compressing objects: 100% (11/11), done.
Writing objects: 100% (16/16), 3.57 KiB | 3.57 MiB/s, done.
Total 16 (delta 7), reused 13 (delta 4), pack-reused 0 (from 0)
remote: Resolving deltas: 100% (7/7), completed with 3 local objects.
remote: 
remote: Create a pull request for 'enh-codespell' on GitHub by visiting:
remote:      https://github.com/yarikoptic/claude-scientific-skills/pull/new/enh-codespell
remote: 
To github.com:yarikoptic/claude-scientific-skills.git
 * [new branch]      enh-codespell -> enh-codespell
branch 'enh-codespell' set up to track 'gh-yarikoptic/enh-codespell'.
❯ gh pr create --repo K-Dense-AI/claude-scientific-skills --title "Add codespell support with configuration and fixes" --body-file .git/pr-description.md --web

Opening github.com/K-Dense-AI/claude-scientific-skills/compare/main...yarikoptic:enh-codespell in your browser.

@TKassis TKassis closed this May 19, 2026
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Suggestion: Add Git LFS to Prerequisites in README? Add SkillKit commands for cross-agent compatibility

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