bootstrap: add automatic .pth write for editable installs so top-level CLI is importable

scripts/bootstrap.sh

@@ -285,19 +285,107 @@ if [[ "$NOINSTALL" != "true" ]]; then  # If not explicitly requested, auto-selec
     # Additional compatibility check: top-level 'CLI' module may be required by
     # older entrypoints or direct imports when running from a development checkout.
     if ! "$VENV_PY" -c 'import importlib,sys; importlib.import_module("CLI")' >/dev/null 2>&1; then
-      echo "Note: top-level 'CLI' module not importable; some entrypoints expect it." >&2
+      echo "Note: top-level 'CLI' module not importable; attempting to add the repo root to venv site-packages via a .pth file so top-level imports work." >&2
 
-      # If this appears to be a development checkout, offer to install editable mode
-      if [[ -d "$REPO/.git" ]] || git -C "$REPO" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-        if [[ "$EDITABLE" == "true" ]]; then
-          echo "Installing project in editable mode to provide top-level 'CLI'..."
-          "$VENV_PY" -m pip install -e "$REPO" || { echo "Editable install failed" >&2; exit 6; }
+      # Try to discover venv site-packages and write a .pth pointing at the repo root
+      site_pkgs=$("$VENV_PY" - <<'PY'
+import site, sysconfig
+out=[]
+try:
+    out.extend(site.getsitepackages())
+except Exception:
+    pass
+try:
+    p = sysconfig.get_paths().get('purelib')
+    if p:
+        out.append(p)
+except Exception:
+    pass
+seen=set(); res=[]
+for x in out:
+    if x and x not in seen:
+        seen.add(x); res.append(x)
+for s in res:
+    print(s)
+PY
+)
+      site_pkg_dir=""
+      while IFS= read -r sp; do
+        if [[ -d "$sp" ]]; then site_pkg_dir="$sp"; break; fi
+      done <<< "$site_pkgs"
+
+      if [[ -n "$site_pkg_dir" ]]; then
+        pth_file="$site_pkg_dir/medeia_repo.pth"
+        if [[ -f "$pth_file" ]]; then
+          if grep -qxF "$REPO" "$pth_file" >/dev/null 2>&1; then
+            echo ".pth already present and contains repo root: $pth_file" >&2
+          else
+            echo "$REPO" >> "$pth_file"
+            echo "Appended repo root to existing .pth: $pth_file" >&2
+          fi
         else
-          if [[ "$QUIET" != "true" && -t 0 ]]; then
-            read -p "Top-level 'CLI' not importable; install project in editable mode now? (Y/n) " devans2
-            if [[ -z "$devans2" || "$devans2" == "y" || "$devans2" == "Y" ]]; then
+          echo "$REPO" > "$pth_file"
+          echo "Wrote .pth adding repo root to venv site-packages: $pth_file" >&2
+        fi
+
+        # Re-check whether 'CLI' is now importable
+        if "$VENV_PY" -c 'import importlib,sys; importlib.import_module("CLI")' >/dev/null 2>&1; then
+          echo "Top-level 'CLI' import works after adding .pth" >&2
+        else
+          echo "Adding .pth did not make top-level 'CLI' importable." >&2
+
+          # Fallback: if this is a git checkout, try editable reinstall or prompt user
+          if [[ -d "$REPO/.git" ]] || git -C "$REPO" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+            if [[ "$EDITABLE" == "true" ]]; then
+              echo "Editable install already requested; attempting editable reinstall for good measure..." >&2
               "$VENV_PY" -m pip install -e "$REPO" || { echo "Editable install failed" >&2; exit 6; }
+              if "$VENV_PY" -c 'import importlib,sys; importlib.import_module("CLI")' >/dev/null 2>&1; then
+                echo "Top-level 'CLI' is now importable after reinstall." >&2
+              else
+                echo "Editable reinstall did not make 'CLI' importable. Please inspect the venv or create an egg-link." >&2
+                exit 6
+              fi
             else
+              if [[ "$QUIET" != "true" && -t 0 ]]; then
+                read -p "Top-level 'CLI' not importable; install project in editable mode now? (Y/n) " devans2
+                if [[ -z "$devans2" || "$devans2" == "y" || "$devans2" == "Y" ]]; then
+                  "$VENV_PY" -m pip install -e "$REPO" || { echo "Editable install failed" >&2; exit 6; }
+                else
+                  echo "Warning: continuing without top-level 'CLI' importable; some entrypoints may fail." >&2
+                fi
+              else
+                echo "Top-level 'CLI' not importable and cannot prompt (quiet mode); aborting." >&2
+                exit 6
+              fi
+            fi
+          else
+            echo "Top-level 'CLI' not importable and not a git checkout; continuing at your own risk." >&2
+          fi
+        fi
+      else
+        echo "Unable to determine site-packages directory to write .pth; skipping .pth fallback." >&2
+        if [[ -d "$REPO/.git" ]] || git -C "$REPO" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+          if [[ "$EDITABLE" == "true" ]]; then
+            echo "Attempting editable install to provide top-level 'CLI'..."
+            "$VENV_PY" -m pip install -e "$REPO" || { echo "Editable install failed" >&2; exit 6; }
+          else
+            if [[ "$QUIET" != "true" && -t 0 ]]; then
+              read -p "Top-level 'CLI' not importable; install project in editable mode now? (Y/n) " devans2
+              if [[ -z "$devans2" || "$devans2" == "y" || "$devans2" == "Y" ]]; then
+                "$VENV_PY" -m pip install -e "$REPO" || { echo "Editable install failed" >&2; exit 6; }
+              else
+                echo "Warning: continuing without top-level 'CLI' importable; some entrypoints may fail." >&2
+              fi
+            else
+              echo "Top-level 'CLI' not importable and cannot prompt (quiet mode); aborting." >&2
+              exit 6
+            fi
+          fi
+        else
+          echo "Top-level 'CLI' not importable and not a git checkout; continuing." >&2
+        fi
+      fi
+    fi
               echo "Continuing without editable install; 'mm' may not work as expected." >&2
             fi
           else