[BUG] Update marketplace" in plugin manager fails with 3 different, contradictory errors for a valid git-based marketplace

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Environment:

• macOS 26.3.1 (build 25D771280a)
• git 2.50.1 (Apple Git-155)
• Marketplace source: git, https://github.com/healthgrades/hg-claude-plugins.git
• Claude Code version: (check Help/About in the app — not retrievable from this session)

Steps to reproduce:

1. Have a git-based marketplace already added and successfully cloned (hg-claude-plugins, registered in ~/.claude/plugins/known_marketplaces.json).
2. Open the Manage Plugins panel → Marketplaces tab.
3. Click the refresh icon next to the marketplace to pick up new upstream commits.

Expected: the tool does a git fetch/pull (or equivalent) against the existing local clone and updates it to the latest commit.

Actual: three different failures across repeated attempts, none of which reflect the real state of the repo:

1. First attempt:

``
✘ Failed to update marketplace(s): Failed to refresh marketplace 'hg-claude-plugins': Failed to clone marketplace repository: Cloning into '/Users/.../hg-claude-plugins'... BUG: refs/files-backend.c:3050: initial ref transaction called with existing refs
``

1. After a machine restart, retrying the same button:

``
✘ ... fatal: destination path '/Users/.../hg-claude-plugins' already exists and is not an empty directory.
``

1. After deleting the local clone directory so a clean clone could occur:

``
✘ ... The marketplace.json file is no longer present in this repository. This marketplace may have been deprecated or moved to a new location. ... You can remove this marketplace with: claude plugin marketplace remove hg-claude-plugins
``

Evidence the repo/file are fine (this is a tool bug, not a repo problem):

• After the "failed" clone, ~/.claude/plugins/marketplaces/hg-claude-plugins/ is a valid, clean git checkout: git status → "up to date with origin/main", git log -1 matches git ls-remote origin main exactly (commit cc52e5098b87...).
• ~/.claude/plugins/marketplaces/hg-claude-plugins/.claude-plugin/marketplace.json exists (14,362 bytes) at the exact path the tool claims is missing.

Impact: Because "Update marketplace" never reports success, ~/.claude/plugins/installed_plugins.json stays pinned to a stale commit (f851622da622 from 2026-06-24) for all plugins from this marketplace (release-ucms-ssp, team-config, announce, jira, qa-steps), even though the marketplace's own git clone already has the newer commit (cc52e5098b87, 2026-07-08) on disk. No supported UI path currently gets installed plugins re-pinned to the newer commit.

Suggested root cause: the refresh flow appears to always attempt a fresh git clone into the marketplace's install directory rather than fetching/pulling an existing clone, and its precondition/error-detection logic (marketplace.json existence check) appears to run against stale or wrong state, producing false-negative errors.

What Should Happen?

The refresh should have done a git fetch + git pull (or fetch + reset to the remote ref) against the existing clone at ~/.claude/plugins/marketplaces/hg-claude-plugins/, since that clone was already there and valid — not attempted a fresh git clone into a directory that already has content. That's the root cause of all three errors: every retry path assumes "no clone exists yet" and tries to create one, so it trips over its own leftover state.

Concretely, the correct flow would have been:

1. Detect the marketplace directory already has a git repo.
2. git fetch origin + git reset --hard origin/main (or equivalent) to bring it to the latest commit — no clone-from-scratch needed.
3. Re-read .claude-plugin/marketplace.json from that updated checkout (which was there the whole time) to get the new plugin listing.
4. Re-pin installed_plugins.json entries for release-ucms-ssp, team-config, etc. to the new commit SHA, and refresh the plugin cache under ~/.claude/plugins/cache/hg-claude-plugins/.../<new-sha>/.

Instead, the tool tried to clone every time, which is why deleting the directory didn't even help — a fresh clone should have succeeded into an empty directory, but instead threw a third, unrelated "marketplace.json missing" error, suggesting the update logic doesn't even wait for its own clone to finish (or checks the wrong path/ref) before validating.

Error Messages/Logs

Steps to Reproduce

Here's a detailed, standalone steps-to-reproduce section:

Steps to reproduce:

1. Add a git-based marketplace (source: https://github.com/healthgrades/hg-claude-plugins.git) and install at least one plugin from it (e.g. release-ucms-ssp@hg-claude-plugins). This creates:

• ~/.claude/plugins/marketplaces/hg-claude-plugins/ — a full git clone of the marketplace repo
• ~/.claude/plugins/known_marketplaces.json — marketplace registration
• ~/.claude/plugins/installed_plugins.json — pins each installed plugin to the commit SHA it was cloned at (e.g. f851622da622, dated 2026-06-24)

1. Let time pass while the upstream repo receives new commits (in this case, a commit cc52e5098b87 landed 2026-07-08 fixing bugs in the very skill installed).
2. Open the Manage Plugins panel → Marketplaces tab.
3. Click the refresh icon next to hg-claude-plugins to pull the new commits.

• Result A: fails with BUG: refs/files-backend.c:3050: initial ref transaction called with existing refs (attempting a fresh clone into the already-populated directory).

1. Restart the machine. Repeat step 4 without changing anything else.

• Result B: fails with fatal: destination path '.../hg-claude-plugins' already exists and is not an empty directory. (confirms it's retrying the same clone-into-existing-dir operation, not a fetch/pull).

1. Manually delete the stale local clone (rm -rf ~/.claude/plugins/marketplaces/hg-claude-plugins) so the next attempt has a truly empty target directory. Repeat step 4.

• Result C: fails with The marketplace.json file is no longer present in this repository. ... You can remove this marketplace with: claude plugin marketplace remove hg-claude-plugins — despite the directory being freshly re-cloned, on origin/main, matching the remote's latest commit exactly, and .claude-plugin/marketplace.json existing on disk at the expected path (verified via git log, git status, git ls-remote, and find/ls on the file).

1. At no point does installed_plugins.json get updated — plugins from this marketplace remain pinned to the original 2026-06-24 commit, even though the local marketplace clone itself is up to date at every stage after step 6.

Note: step 6 is a destructive workaround attempted only after step 5 failed identically post-restart — it did not fix the underlying issue and produced a third, distinct false error instead.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

Claude 1.19367.0 (1a5be1) 2026-07-07T05:45:41.000Z

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_