This repo: https://github.com/DISTRHO/MVerb.git (packaged in audio-overlay) Can't be recursively cloned by git-r3 as at commit 42a9e910fd69ca72b6d211f15ad2ecef7b17ed5d, because stumbles trying to fetch commit 856c759e1e360b0a766f61bb2b2cfffe15790368 in pugl, which is not included to any branch, but referenced by submodules chain (mverb->dpf->pugl). However, "git clone --recursive" is fine. After cloning DISTRHO_pugl itself, I was able to make necessary commit available by doing "git fetch origin 856c759e1e360b0a766f61bb2b2cfffe15790368". After I repeated same command inside copy in git3-src (by git-r3), with "origin" replaced to full clone url, git-r3 could detect necessary commit and mverb package was successfully merged. Reproducible: Always Steps to Reproduce: 1. Create git-r3 based ebuild and edit: EGIT_REPO_URI=https://github.com/DISTRHO/MVerb.git EGIT_COMMIT=42a9e910fd69ca72b6d211f15ad2ecef7b17ed5d 2. Try to emerge. Actual Results: * Fetching https://github.com/DISTRHO/pugl.git ... git fetch https://github.com/DISTRHO/pugl.git --prune +refs/heads/*:refs/heads/* +refs/tags/*:refs/tags/* +refs/notes/*:refs/notes/* +refs/pull/*/head:refs/pull/* +HEAD:refs/git-r3/HEAD git update-ref --no-deref refs/git-r3/media-plugins/mverb/0/dpf/dgl_src_pugl-upstream/__main__ 856c759e1e360b0a766f61bb2b2cfffe15790368 fatal: update_ref failed for ref 'refs/git-r3/media-plugins/mverb/0/dpf/dgl_src_pugl-upstream/__main__': cannot update ref 'refs/git-r3/media-plugins/mverb/0/dpf/dgl_src_pugl-upstream/__main__': trying to write ref 'refs/git-r3/media-plugins/mverb/0/dpf/dgl_src_pugl-upstream/__main__' with nonexistent object 856c759e1e360b0a766f61bb2b2cfffe15790368 * ERROR: media-plugins/mverb-9999::audio-overlay failed (unpack phase): * Referencing 856c759e1e360b0a766f61bb2b2cfffe15790368 failed (wrong ref?). Expected Results: Should be able to fetch any commit as long as it's not completely cleaned out at git source. "git branch -a --contains <commit-id>" will not list anything for orphane commit until it's checked out (detached HEAD).