fix(session): make the remote-session bootstrap reachable and honest

.claude/hooks/session-start.sh

@@ -46,7 +46,26 @@ set -euo pipefail
 
 VENV="${PYAUTO_SESSION_VENV:-$HOME/.pyauto/session-py312}"
 BASE_DEPS=(pytest PyYAML)
-EXTRAS_FILE="${CLAUDE_PROJECT_DIR:-$PWD}/.claude/session-python.txt"
+
+# Which checkout is this copy of the hook installed in?
+#
+# NOT $CLAUDE_PROJECT_DIR. That is the session's project directory, which equals
+# the repo only when the session holds exactly ONE repo. A session scoped to
+# several organs clones them side by side under the project directory
+# (/home/user/PyAutoMind, /home/user/PyAutoBrain, ...), and then
+# $CLAUDE_PROJECT_DIR is their parent — so reading session-python.txt from it
+# found nothing, silently, in exactly the sessions that hold the most repos.
+#
+# Derive it from where this script actually is, in both the installed and the
+# canonical location.
+HOOK_SELF="$(readlink -f "$0")"
+case "$(dirname "$HOOK_SELF")" in
+    */.claude/hooks) REPO_DIR="$(cd "$(dirname "$HOOK_SELF")/../.." && pwd)" ;;
+    */policy)        REPO_DIR="$(cd "$(dirname "$HOOK_SELF")/.."    && pwd)" ;;
+    *)               REPO_DIR="${CLAUDE_PROJECT_DIR:-$PWD}" ;;
+esac
+WORKSPACE_ROOT="$(dirname "$REPO_DIR")"
+EXTRAS_FILE="$REPO_DIR/.claude/session-python.txt"
 
 # stderr, not stdout: a SessionStart hook's stdout is fed to the agent as
 # session context.
@@ -173,6 +192,107 @@ retool_uv_tools() {
     done
 }
 
+# 4. Honest git history.
+#
+# A remote session clones shallow. `git merge-base --is-ancestor` then LIES
+# across the graft boundary: it reports "not an ancestor" for a commit whose
+# ancestry is simply not in the clone, and the ship/close-out skills act on that
+# answer. A completion record already logged this the hard way
+# (complete/2026/08/status-sh-repos-missing-source.md, "environment note").
+#
+# These repos are small (single-digit MB of .git), so unshallowing costs a
+# couple of seconds once per container and removes a whole class of wrong
+# answer. Bounded and non-fatal: a slow or blocked network leaves a shallow
+# clone and a warning, never a failed session start.
+ensure_full_clone() {
+    local repo
+    for repo in "$WORKSPACE_ROOT"/*/; do
+        [ -e "${repo}.git/shallow" ] || continue
+        log "unshallowing $(basename "$repo") (shallow clones make ancestry checks lie)"
+        if timeout 120 git -C "$repo" fetch --unshallow --quiet 2>/dev/null \
+           || timeout 120 git -C "$repo" fetch --depth=2147483647 --quiet 2>/dev/null; then
+            log "  $(basename "$repo"): full history ($(git -C "$repo" rev-list --count HEAD 2>/dev/null) commits)"
+        else
+            log "  WARNING: $(basename "$repo") is still shallow — run 'git fetch --unshallow' before trusting any ancestry check"
+        fi
+    done
+}
+
+# 5. Make the NEXT session in this container start correctly.
+#
+# Claude Code registers project hooks from the session's project directory. In a
+# one-repo session that IS the repo, and `<repo>/.claude/settings.json` is found.
+# In a session holding several organs the project directory is their parent,
+# which is not a repo and has no `.claude/` — so none of the per-repo hooks are
+# registered and none of this script runs. That is why a multi-repo session came
+# up on the container's Python 3.11: not a broken hook, an unreachable one.
+#
+# A repo cannot ship a file into its own parent, so install it at run time. The
+# settings we write fan out to every sibling repo's own hook, so the layout
+# stays "each repo owns its hook" and this file stays generated-from-one-source.
+# It takes effect on the next session start in this container.
+install_workspace_settings() {
+    # Only in the multi-repo layout: when the project dir IS this repo, Claude
+    # Code already found the repo's own settings and there is nothing to add.
+    [ -n "${CLAUDE_PROJECT_DIR:-}" ] || return 0
+    [ "$(readlink -f "$CLAUDE_PROJECT_DIR")" != "$(readlink -f "$REPO_DIR")" ] || return 0
+
+    local settings="$CLAUDE_PROJECT_DIR/.claude/settings.json"
+    local fanout="$CLAUDE_PROJECT_DIR/.claude/hooks/session-start.sh"
+    [ -w "$CLAUDE_PROJECT_DIR" ] || { log "WARNING: $CLAUDE_PROJECT_DIR not writable; multi-repo sessions will keep skipping the hook"; return 0; }
+
+    mkdir -p "$(dirname "$fanout")"
+    cat >"$fanout" <<'FANOUT'
+#!/usr/bin/env bash
+# GENERATED at session start by a PyAuto repo's own session-start hook.
+# Runs every sibling repo's hook, because the workspace root is not a repo and
+# therefore has no hook of its own. Each repo's hook is idempotent, so the
+# second and later ones cost ~0.2s.
+set -u
+ROOT="$(cd "$(dirname "$(readlink -f "$0")")/../.." && pwd)"
+for repo in "$ROOT"/*/; do
+    hook="${repo}.claude/hooks/session-start.sh"
+    [ -x "$hook" ] || continue
+    CLAUDE_PROJECT_DIR="${repo%/}" "$hook" || \
+        printf '[session-start] WARNING: %s failed\n' "$hook" >&2
+done
+FANOUT
+    chmod 0755 "$fanout"
+
+    if [ ! -f "$settings" ]; then
+        cat >"$settings" <<'SETTINGS'
+{
+  "hooks": {
+    "SessionStart": [
+      {
+        "hooks": [
+          {
+            "type": "command",
+            "command": "$CLAUDE_PROJECT_DIR/.claude/hooks/session-start.sh"
+          }
+        ]
+      }
+    ]
+  }
+}
+SETTINGS
+        log "installed $settings — multi-repo sessions in this container now run the hook"
+    fi
+}
+
+# Git history and hook reachability have nothing to do with the interpreter, so
+# they run first and unconditionally: a container where the 3.12 venv cannot be
+# built still wants honest ancestry and a hook that fires next session.
+ensure_full_clone
+install_workspace_settings
+
+# PYAUTO_SESSION_SKIP_PYTHON=1 stops here — the seam the hook's own tests use to
+# exercise the legs above without building an interpreter.
+if [ "${PYAUTO_SESSION_SKIP_PYTHON:-}" = "1" ]; then
+    log "PYAUTO_SESSION_SKIP_PYTHON=1 — leaving the interpreter alone"
+    exit 0
+fi
+
 if ensure_venv; then
     ensure_repo_extras
     point_system_default "$(readlink -f "$VENV/bin/python")"
@@ -184,6 +304,9 @@ if ensure_venv; then
             echo "export PYAUTO_SESSION_PY312=\"$VENV\""
             echo "export VIRTUAL_ENV=\"$VENV\""
             echo "export PATH=\"$VENV/bin:\$PATH\""
+            # The workspace root, so the Brain's shell/python resolvers agree
+            # with the session instead of each re-deriving it.
+            echo "export PYAUTO_ROOT=\"$WORKSPACE_ROOT\""
         } >>"$CLAUDE_ENV_FILE"
     fi
     log "default python is now $("$VENV/bin/python" -V 2>&1) ($VENV/bin)"

dashboard.html

@@ -185,7 +185,7 @@
 </head>
 <body>
 <header class="hero"><span class="orb"><svg class="mark" viewBox="0 0 48 48" fill="none" stroke="currentColor" stroke-width="1.3" stroke-linecap="round" stroke-linejoin="round" aria-hidden="true"><circle cx="24" cy="24" r="20.4"/><path d="M20.2,37.6 L20.2,33.6 C20.2,32.4 19.4,31.6 18.4,30.8 C16.8,29.6 15.8,28.2 15.6,26.6 C15.5,25.6 14.9,25.2 13.9,24.9 C12.6,24.5 12.3,23.7 13.0,22.7 C13.8,21.6 14.5,20.6 14.6,19.4 C15.0,15.4 18.2,12.2 22.4,11.8 C27.2,11.3 31.6,14.6 32.3,19.2 C32.8,22.4 31.6,25.0 30.6,27.0 C29.9,28.4 29.6,29.6 29.6,31.2 L29.6,37.6"/><circle cx="24.6" cy="19.6" r="4.4"/><path d="M22.5,19.7 L24.0,21.3 L26.8,18.1"/><path d="M34.2,16.5 L38.8,16.5 M35.2,21.0 L39.4,21.0 M33.6,25.5 L37.2,25.5"/><g fill="currentColor" stroke="none"><circle cx="40.1" cy="16.5" r="1.4"/><circle cx="40.7" cy="21.0" r="1.4"/><circle cx="38.5" cy="25.5" r="1.4"/></g></svg></span><h1>PyAuto<b>Mind</b><span class="kind">Dashboard</span></h1><div class="rule"></div><p class="tag">Intent. Priority. Flow.</p></header><p class="lede">Every task the Mind is holding. Tap a task's 📋 and its <code>/start_dev</code> command is on your clipboard — paste it into a Claude Code chat to route Claude straight to that task. <a href="#recent">Recent</a> is the same work by date — what has been happening rather than what to do next.</p>
-<ul class="stats"><li><b>1</b><span>In flight</span></li><li><b>3</b><span>Parked</span></li><li><b>5</b><span>Planned</span></li><li><b>133</b><span>Backlog</span></li></ul>
+<ul class="stats"><li><b>1</b><span>In flight</span></li><li><b>3</b><span>Parked</span></li><li><b>5</b><span>Planned</span></li><li><b>134</b><span>Backlog</span></li></ul>
 <div class="fresh"><p><b>Last updated 2026-08-26.</b> This page is generated from <code>active/</code>, <code>draft/</code> and the registry files, so it is only as current as they are. <code>dashboard_refresh.yml</code> re-renders it on every push to <code>main</code> — that heals a stale page, but not a stale prompt: a task that shipped without its prompt advancing to <code>complete/</code> keeps rendering here as pickable backlog. Reconciling those is the refresh below.</p>
 <div class="task"><button class="copy" data-cmd="Bring the PyAutoMind dashboard up to date. Work in the PyAutoMind checkout:
 
@@ -250,9 +250,9 @@ <h2>Planned <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoMind/blob
 <div class="task"><button class="copy" data-cmd="/route start the planned PyAutoMind task latent-nan-guard-honest-run — its record is in planned.md" aria-label="Copy the Claude command">📋</button><p><b>latent-nan-guard-honest-run</b><span class="facets"> — planned 2026-07-22</span></p></div>
 </details>
 <h2>Backlog <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoMind/tree/main/draft">markdown version</a></h2>
-<p class="muted">133 filed prompts, not started — sorted most-pickable first (priority, then size). 25 of them belong to an epic and are listed only under Epics below.</p>
+<p class="muted">134 filed prompts, not started — sorted most-pickable first (priority, then size). 25 of them belong to an epic and are listed only under Epics below.</p>
 <details>
-<summary>feature — 27</summary>
+<summary>feature — 28</summary>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autoarray/numba_cpu_likelihood_mge_convolution_and_caching.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autoarray/numba_cpu_likelihood_mge_convolution_and_caching.md">Numba CPU likelihood phase 1: batched MGE convolution + operated-matrix caching</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autoarray</span><span class="pill n">medium</span><span class="pill n">supervised</span><span class="pill r">high</span></span></p></div>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autoarray/rectangular_bilinear_rtu_mesh_split.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autoarray/rectangular_bilinear_rtu_mesh_split.md">Rectangular mesh split: Bilinear (fast CPU default) vs RTU (advanced/GPU)</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autoarray</span><span class="pill n">medium</span><span class="pill n">supervised</span><span class="pill r">high</span></span></p></div>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autoarray/numba_cpu_likelihood_kernel_cdf_fast_path.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autoarray/numba_cpu_likelihood_kernel_cdf_fast_path.md">Numba CPU likelihood phase 2: kernel-CDF numba fast path (the 49-88% lever)</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autoarray</span><span class="pill y">large</span><span class="pill n">supervised</span><span class="pill r">high</span></span></p></div>
@@ -269,6 +269,7 @@ <h2>Backlog <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoMind/tree
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autofit_assistant/remote_mcp_deployment_tiers.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autofit_assistant/remote_mcp_deployment_tiers.md">Remote-MCP deployment tiers (2 + 3) for the results-inspector server</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autofit_assistant</span><span class="pill y">large</span><span class="pill r">human-required</span><span class="pill n">normal</span></span></p></div>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autolens_profiling/search_settings_estimation_infrastructure.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autolens_profiling/search_settings_estimation_infrastructure.md">Search settings-estimation + profiling infrastructure (n_starts / batch_size / n_batch)</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autolens_profiling</span><span class="pill y">large</span><span class="pill n">supervised</span><span class="pill n">normal</span></span></p></div>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autolens_workspace/oversampled_psf_dataset_adoption.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autolens_workspace/oversampled_psf_dataset_adoption.md">Adopt oversampled PSFs in the start-here dataset chain (option a)</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autolens_workspace</span><span class="pill y">large</span><span class="pill n">supervised</span><span class="pill n">normal</span></span></p></div>
+<div class="task"><button class="copy" data-cmd="/start_dev draft/feature/pyautobrain/board_without_gh.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/pyautobrain/board_without_gh.md">The Brain board should work in a session that has no <code>gh</code></a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">pyautobrain</span><span class="pill y">large</span><span class="pill n">supervised</span><span class="pill n">normal</span></span></p></div>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autoarray/rectangular_multi_submesh.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autoarray/rectangular_multi_submesh.md">Follow-up to <code>rectangular_adapt_cdf.md</code> (issue #322) and Path A</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autoarray</span><span class="pill r">too-large</span><span class="pill n">supervised</span><span class="pill n">normal</span></span></p></div>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autogalaxy/piemass_potential.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autogalaxy/piemass_potential.md"><code>PIEMass.potential_2d_from</code>: implement the missing lensing potential</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autogalaxy</span><span class="pill r">too-large</span><span class="pill n">supervised</span><span class="pill n">normal</span></span></p></div>
 <div class="task"><button class="copy" data-cmd="/start_dev draft/feature/autolens_jax_joss/autolens_jax_joss_benchmark_repo.md" aria-label="Copy the Claude command">📋</button><p><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/autolens_jax_joss/autolens_jax_joss_benchmark_repo.md">autolens_jax_joss benchmark repo + real-data start_here pairing</a><span class="tags"><span class="pill w">✨ feature</span><span class="pill">autolens_jax_joss</span><span class="pill r">too-large</span><span class="pill n">supervised</span><span class="pill n">normal</span></span></p></div>
@@ -396,6 +397,12 @@ <h2>Backlog <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoMind/tree
 <td class="pick"><button class="copy" data-cmd="/start_dev draft/bug/workspaces/gradient_pixelization_pin_residual_drift.md" aria-label="Copy the Claude command">📋</button></td>
 </tr>
 <tr>
+<td class="when">2026-08-26</td>
+<td class="what">filed</td>
+<td><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/feature/pyautobrain/board_without_gh.md">The Brain board should work in a session that has no <code>gh</code></a></td>
+<td class="pick"><button class="copy" data-cmd="/start_dev draft/feature/pyautobrain/board_without_gh.md" aria-label="Copy the Claude command">📋</button></td>
+</tr>
+<tr>
 <td class="when">2026-08-24</td>
 <td class="what">filed</td>
 <td><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/maintenance/ci/wiki_currency_check_version_gate.md">wiki-currency's --check-version gate rots on every library main merge</a></td>
@@ -443,7 +450,7 @@ <h2>Backlog <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoMind/tree
 <td><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/maintenance/workspaces/pynufft_removal_downstream_residue.md">pynufft removal: unswept downstream residue (1 hard break + stale…</a></td>
 <td class="pick"><button class="copy" data-cmd="/start_dev draft/maintenance/workspaces/pynufft_removal_downstream_residue.md" aria-label="Copy the Claude command">📋</button></td>
 </tr>
-<tr>
+<tr hidden>
 <td class="when">2026-08-23</td>
 <td class="what">filed</td>
 <td><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/maintenance/workspaces/pynufft_removal_downstream_residue_phase_3_ci_install_docs.md">Phase 3: stop installing pynufft in Hands/Heart CI and PyAutoCTI…</a></td>
@@ -683,12 +690,6 @@ <h2>Backlog <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoMind/tree
 <td><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/research/autolens_profiling/cluster_gradient_search_benchmark.md">Cluster-scale gradient-search benchmark (Prodigy vs Nautilus…</a></td>
 <td class="pick"><button class="copy" data-cmd="/start_dev draft/research/autolens_profiling/cluster_gradient_search_benchmark.md" aria-label="Copy the Claude command">📋</button></td>
 </tr>
-<tr hidden>
-<td class="when">2026-07-30</td>
-<td class="what">filed</td>
-<td><a href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/draft/docs/workspaces/plot_coverage_followups.md">plot coverage — follow-ups deferred from plot-coverage-gaps</a></td>
-<td class="pick"><button class="copy" data-cmd="/start_dev draft/docs/workspaces/plot_coverage_followups.md" aria-label="Copy the Claude command">📋</button></td>
-</tr>
 </table>
 <button class="more" data-page="10">… 10 more (40 left)</button>
 <h2>Epics <a class="mdsrc" href="https://github.com/PyAutoLabs/PyAutoMind/blob/main/epics.md">markdown version</a></h2>