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docs: track symlinked Pi package install corruption

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2026-09-03 23:53:38 -04:00
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During the Orca polling fix on 02SEP2026, Bash tool calls configured with `cwd` beneath `/srv/data/code/jb-pi/harness-tools/.worktrees/fix-orca-polling` ran from the primary checkout instead. A `pwd` probe reproduced the mismatch, and later install and commit commands targeted the primary checkout until they were rerun with an explicit `cd` or `git -C`. The mistaken commit was reset immediately without discarding the pre-existing working changes. Reproduce this with a disposable hidden worktree and require the tool to either honor the requested directory or fail before executing the command. Cover both workspace and nested package directories; keep explicit `cd` and `git -C` as the workaround until the regression is fixed.
## Canonicalize symlinked Pi npm install roots
Publishing `@jbcode/pi-interactive-subagents@3.7.4` exposed a Pi package-manager failure when `~/.pi` resolves through `/home/jb/data/.home-dotdirs/.pi`. Pi 0.84.4 invoked npm 12.0.2 with `--prefix /home/jb/.pi/agent/npm` from the repository cwd. npm rewrote the lockfile root as `file:../../../data/.home-dotdirs/.pi/agent/npm`, recursively duplicated that path until the lock contained 12,576 entries and 18 MB of data, and then failed with `ENOENT` during reification. Canonicalizing the npm root, regenerating both lockfiles from that directory, and installing once restored the 124-entry lock and all configured packages. Update Pi's npm package execution to use the canonical install root as its cwd, add a symlinked-agent-directory regression test, and ensure interrupted installs terminate their package-manager children before another reconciliation begins.
## Merge `_workflows` reference runtime into `workflow`
`extensions/_workflows` was retained only as a reference while `extensions/workflow` was developed, but `workflow` still imports its runner, model, prompt, and serialization modules. Move the required code under `extensions/workflow`, remove obsolete model-authored workflow surfaces, update tests and documentation, and then delete the reference directory. Until that work is complete, `@jbcode/pi-workflow` must remain a private Bun workspace and `extensions/_workflows` must remain excluded from workspaces and publication. Acceptance requires `bun pm pack` for `workflow` to contain every runtime import without reaching outside the package root, followed by an isolated Pi package smoke test.