Claude Code's parallel-subagent worktree cleanup deleted the main .git directory and entire working tree — irrecoverable repo loss (GitHub #48927)

On April 16, 2026, a Claude Code user (version 2.1.109, Opus model, Ubuntu/Debian Linux, Anthropic API) filed GitHub issue #48927 describing total loss of a git repository after running two successive rounds of parallel subagents isolated with Claude Code's `isolation: worktree` feature. The first round — four subagents implementing modules M06, M02, M01 and M04 on branch `dev/mode-2` — finished after about 15 minutes and produced four successful commits (`55a4fe3` through `88b6f9c`). A second round of four subagents (M07, M03, M05, M01-deploy) was then launched; when it finished about eight minutes later, the next git command failed with `fatal: not a git repository (or any of the parent directories): .git`. The repository's `.git` directory, all pre-existing source code, `docs/`, `tests/`, `README.md`, configuration files, and the four commits from the first round were gone. Only a few files written by the second round's subagents — `install.sh`, `uninstall.sh`, `pyproject.toml` — survived. The reporter's diagnosis, backed by detailed reproduction steps, was that the worktree cleanup mechanism operated on the main working tree rather than confining itself to the isolated worktree directories — a scope/path-confusion bug in the cleanup logic rather than a single bad command. No remote backup existed, so the loss was irrecoverable. GitHub labeled the issue `data-loss` and `has repro`; it was closed as not planned.