[bug] install-plugin.sh --postgres leaves mixed package versions in the deps directory on upgrade #573

What happened

Upgrading an existing PostgreSQL plugin install from 4.21.0 to 4.22.0 with bash scripts/install-plugin.sh failed at verification step 6/7:

ImportError: tokenizers>=0.22.0,<=0.23.0 is required for a normal functioning of this module, but found tokenizers==0.23.2.
[FAIL] sentence-transformers

scripts/setup.sh:224 (the PostgreSQL path) runs python3 -m pip install -q --target "$DEPS_DIR" --no-deps --require-hashes -r requirements/setup.txt directly into the persistent $CLAUDE_PLUGIN_DATA/deps. Without --upgrade, pip keeps every top-level entry that already exists and prints WARNING: Target directory .../deps/<pkg> already exists. Specify --upgrade to force replacement. It skips the package directories but adds the new versioned *.dist-info next to the old ones. After the upgrade, the deps directory held the old code under new metadata:

scripts/setup.py:224 (the SQLite path) makes the same direct --target call. Its comment says skip-if-present is deliberate for concurrency (ADR-0749). That holds on a first install, not across versions.

The launcher already has the correct upgrade path: scripts/launcher_deps_install.py installs into a scratch target, commits entry by entry with rollback (commit_entry), and prunes superseded *.dist-info (_commit_resolved_entries). The install scripts bypass it.

Reproduction steps

1. Plugin 4.21.0 installed with --postgres, deps populated in ~/.claude/plugins/data/hypermnesia-mcp-cortex-plugins/deps.
2. claude plugin update hypermnesia-mcp@cortex-plugins → 4.22.0.
3. CLAUDE_PLUGIN_ROOT=<4.22.0> CLAUDE_PLUGIN_DATA=<data> bash scripts/install-plugin.sh.
4. Step 3/7 prints the already exists warnings, and step 6/7 fails on sentence-transformers.

Expected behavior

An upgrade leaves exactly one version of each package in the deps directory, the one pinned by requirements/setup.txt, and verification passes. Workaround used on 2026-09-15: install into a fresh directory (pip install --target deps.new ... -r requirements/setup.txt), check it through the launcher and a real embedding, then swap it in. The re-run of install-plugin.sh then passed all 7 steps.

Environment

• macOS 26, Python 3.14.4, PostgreSQL 17.9
• Cortex 4.21.0 → 4.22.0

Severity

High (every upgrade that changes a pinned dependency breaks the embedding stack until the deps directory is rebuilt by hand)

Evidence required to close

A test that upgrades a deps directory holding version N of a package to the version N+1 pinned in requirements/setup.txt, through both setup.sh and setup.py, and asserts that exactly one *.dist-info per distribution remains and matches the pin. Both scripts should route through the launcher's scratch-and-commit install instead of a direct --target.