Beta known issues (1.0.1) — second-user git-context, residual author paths, default project name

[jessekemp1]

Tracked known issues for the 1.0.1 beta. None are crashes — all degrade gracefully. Surfaced in the PR #5 ship-readiness review.

1. Intelligence git-context is empty for a "folder of independent repos" layout

api/routes/intelligence.py reason_query runs git log/diff with cwd=workspace_root + a rel pathspec — the monorepo model (works for the author's ~/Dev monorepo). For the documented second-user layout (root is a plain folder where each child is its own repo), the root isn't a git repo, so both git calls return non-zero and the "RECENT COMMITS / uncommitted changes" context section is always empty. No crash.
Fix: handle both layouts — run git inside the discovered repo path (cwd=proj["path"], no pathspec) when the child is itself a repo; otherwise fall back to root + pathspec. /projects already uses the cwd=repo-path pattern.

2. Residual author-specific paths outside the de-authoring diff

• NEXT_SESSION_FILES (api/bridge_endpoint.py) hardcodes cortex, Vortex/backend, alpha_arena under the workspace root, so a second user's Conductor gets the author's subpaths.
• /health service checks reference Vortex backend/frontend + alpha_arena; an iTerm-signal path parses "/Dev/" literally.
  Fix: derive from config.discover_projects() / gate behind existence checks so they no-op cleanly for other users.

3. Author's auto-default project name shifted from "cortex" to the workspace dir name

With CORTEX_ROOT_DIR=~/Dev (a git monorepo), _detect_current_project() now returns "Dev" instead of the old hardcoded "cortex". Intentional de-authoring side effect, but a silent default-project change for the original author.
Fix: set CORTEX_DEFAULT_PROJECT=cortex to restore; document the env var in .env.example.

[jessekemp1]

First beta-user sandbox verification (v1.0.1)

Ran BETA_ONBOARDING.md end-to-end in an isolated sandbox as a brand-new second user: fresh clone of the v1.0.1 tag, fresh venv, throwaway CORTEX_ROOT_DIR with two git repos, HOME-isolated state.

Works ✅

• git clone (anonymous, public) + python -m venv + pip install -e . → clean, all deps incl. scikit-learn/scipy, no errors, no proxy timeout.
• cortex init → creates the state dir with clear output + next steps.
• cortex onboard → discovered exactly the 2 sandbox repos, seeded 4 memories + 37 anti-pattern seeds. No author-project leakage — the de-authoring works for a real second user.
• cortex doctor → 5/6 PASS (Python 3.14, anthropic, sklearn, API key, state dir).
• cortex status → works without the bridge; shows the 2 projects, integrations 4/4.
• State fully isolated to the sandbox; the author's real ~/.cortex was untouched (0 leaked entries).

New first-run UX friction (not blockers)

1. cortex doctor reports overall "Some checks FAILED" when the only failure is "bridge :8765 not running". BETA_ONBOARDING runs doctor (step 6) before the "Start the Bridge" section, so a fresh user is guaranteed to see a red FAIL on a step they haven't done yet. Suggest: treat bridge-down as a WARN with the start command, or start the bridge during onboarding.
2. First cortex status is dominated by host-process noise. A brand-new user's headline is "147 alerts / NEXT ACTION: Address zombie_process alerts" about machine processes (read from the live OS process table) — not their projects. Alarming first impression. Suggest: suppress/deprioritize host-process alerts on a fresh install, or don't make them the top NEXT ACTION.
3. Bridge port 8765 is hardcoded (no env override) — fine for a solo user but blocks running two instances / testing. Consider a CORTEX_BRIDGE_PORT.
4. CORTEX_STATE_DIR / CORTEX_HOME override exists (state_paths.py) but isn't documented in BETA_ONBOARDING, and some modules bypass it (hardcode Path.home()/.cortex). Doc + consistency.

Bridge/MCP record + recall (POST /decisions/learning, cortex_intelligence) were validated end-to-end separately; not re-tested here because port 8765 was occupied by another running instance.

Verdict: install + onboarding + second-user scoping are solid — ship-ready for beta. The items above are polish.