fix: dependency installation gaps in Plugin Store and first-time install (#385)

* fix: install plugin dependencies through root-visible installer in Plugin Store

install_plugin/update_plugin (store_manager.py) installed requirements.txt
with a bare `pip3` off PATH, bypassing the root-visible installer added in
#380 for the "Reinstall Plugin Deps" button. Two bugs stacked: (1) `pip3`
can resolve to a different Python install than the one that actually runs
ledmatrix.service, and (2) even when it resolves correctly, ledmatrix-web
runs as a non-root user so the package lands in that user's local
site-packages, invisible to root-run ledmatrix.service. Either way the
install reports success and writes the .dependencies_installed hash marker,
so plugin_loader's own (correct) install-on-load path skips reinstalling —
leaving the dependency permanently missing until a user finds and clicks
the separate "Reinstall Plugin Deps" tool. This is why users kept hitting
"No module named 'astral'" for the weather plugin even after installing it
from the Store.

Extracts the sudo-wrapper-then-fallback install logic from api_v3.py's
_pip_install_requirements into src/common/permission_utils.py as
install_requirements_file, and routes store_manager.py's dependency
installation through it so the automatic Store install/update path now
matches the manual "Reinstall Plugin Deps" path.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01X1NnDduw53kTe67i5zWwYx

* chore: suppress Codacy false-positive on subprocess.run in install_requirements_file

Codacy's generic subprocess-security rule (Bandit B603 equivalent) flagged
the pip/sudo subprocess.run calls in install_requirements_file for lacking a
"static string argument" — the standard pattern-based flag for any
subprocess.run() call with a variable in its argv list. Both calls use
list-form argv (no shell=True, so no shell-injection surface), and the only
dynamic value is req_file, a Path built internally by callers rather than
raw external input; safe_pip_install.sh independently re-validates it before
installing anything as root. Suppresses with inline `# nosec B603` comments
matching this codebase's existing convention (see permission_utils.py's own
PROTECTED_SYSTEM_DIRECTORIES, display_manager.py, sync_manager.py, etc.).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01X1NnDduw53kTe67i5zWwYx

* fix: first-time install script fails on apt-managed requests package

web_interface/requirements.txt and requirements.txt both pin
requests>=2.33.0,<3.0.0, but Raspberry Pi OS ships an apt-managed
python3-requests with no pip RECORD file. Upgrading it via plain
`pip install` aborts with "uninstall-no-record-file" because pip refuses to
uninstall a package it has no record of, in place — which is exactly the
"Some web interface dependencies failed to install" warning first-time
install hits.

scripts/install_dependencies_apt.py and scripts/fix_perms/safe_pip_install.sh
already work around this with --ignore-installed (lets pip lay the new
version down in /usr/local, shadowing the apt copy, instead of trying to
remove it first). first_time_install.sh's own direct pip invocations —
the per-package requirements.txt loop, the web_interface/requirements.txt
install, and the requirements_web_v2.txt fallback — didn't have it. Adds
--ignore-installed to all three so first-time install no longer fails on
this well-known apt/pip conflict.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01X1NnDduw53kTe67i5zWwYx

* chore: add nosemgrep to subprocess.run calls Codacy still flagged

The prior # nosec B603 comments suppressed Bandit's check but Codacy's
semgrep-based rule ("subprocess function 'run' without a static string")
kept flagging the same two lines as a critical security issue even after
that fix landed. install_dependencies_apt.py's _run() already needed both
tags together (# nosec B603 B607 ... # nosemgrep) for the identical
subprocess.run pattern, so apply the same double suppression here.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01X1NnDduw53kTe67i5zWwYx

* fix: add --ignore-installed to install_requirements_file fallback path

CodeRabbit review caught this (confirming a gap already flagged in
conversation): the non-sudo fallback pip install in install_requirements_file
was missing --ignore-installed, unlike the sudo-wrapper branch and
safe_pip_install.sh. Without it, the same apt/pip RECORD-file conflict this
PR fixes elsewhere (first_time_install.sh, install_dependencies_apt.py) could
still hit installs that fall back to this path (e.g. a plugin's
requirements.txt on a host where safe_pip_install.sh isn't set up yet).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01X1NnDduw53kTe67i5zWwYx

---------

Co-authored-by: Claude <noreply@anthropic.com>

first_time_install.sh

@@ -726,7 +726,11 @@ if [ -f "$PROJECT_ROOT_DIR/requirements.txt" ]; then
         
         if command -v timeout >/dev/null 2>&1; then
             # Use timeout if available (10 minutes = 600 seconds)
-            if timeout 600 python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --verbose "$line" > "$INSTALL_OUTPUT" 2>&1; then
+            # --ignore-installed: apt-managed packages (e.g. python3-requests)
+            # ship no pip RECORD file, so upgrading them would otherwise abort
+            # with "uninstall-no-record-file"; this lays the new version down
+            # alongside instead of trying to uninstall the apt copy first.
+            if timeout 600 python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --ignore-installed --verbose "$line" > "$INSTALL_OUTPUT" 2>&1; then
                 INSTALL_SUCCESS=true
             else
                 EXIT_CODE=$?
@@ -734,7 +738,7 @@ if [ -f "$PROJECT_ROOT_DIR/requirements.txt" ]; then
                     echo "✗ Timeout (10 minutes) installing: $line"
                     echo "  This package may require building from source, which can be slow on Raspberry Pi."
                     echo "  You can try installing it manually later with:"
-                    echo "    python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --verbose '$line'"
+                    echo "    python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --ignore-installed --verbose '$line'"
                 else
                     echo "✗ Failed to install: $line (exit code: $EXIT_CODE)"
                 fi
@@ -742,7 +746,7 @@ if [ -f "$PROJECT_ROOT_DIR/requirements.txt" ]; then
         else
             # No timeout command available, install without timeout
             echo "  Note: timeout command not available, installation may take a while..."
-            if python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --verbose "$line" > "$INSTALL_OUTPUT" 2>&1; then
+            if python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --ignore-installed --verbose "$line" > "$INSTALL_OUTPUT" 2>&1; then
                 INSTALL_SUCCESS=true
             else
                 EXIT_CODE=$?
@@ -794,7 +798,7 @@ if [ -f "$PROJECT_ROOT_DIR/requirements.txt" ]; then
         echo "  1. Ensure you have enough disk space: df -h"
         echo "  2. Check available memory: free -h"
         echo "  3. Try installing failed packages individually with verbose output:"
-        echo "     python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --verbose <package>"
+        echo "     python3 -m pip install --break-system-packages --no-cache-dir --prefer-binary --ignore-installed --verbose <package>"
         echo "  4. For packages that build from source (like numpy), consider:"
         echo "     - Installing pre-built wheels: python3 -m pip install --only-binary :all: <package>"
         echo "     - Or installing via apt if available: sudo apt install python3-<package>"
@@ -816,7 +820,10 @@ echo ""
 # Install web interface dependencies
 echo "Installing web interface dependencies..."
 if [ -f "$PROJECT_ROOT_DIR/web_interface/requirements.txt" ]; then
-    if python3 -m pip install --break-system-packages --prefer-binary -r "$PROJECT_ROOT_DIR/web_interface/requirements.txt"; then
+    # --ignore-installed: apt-managed packages (e.g. python3-requests) ship no
+    # pip RECORD file, so upgrading them to the version pinned here would
+    # otherwise abort the whole install with "uninstall-no-record-file".
+    if python3 -m pip install --break-system-packages --prefer-binary --ignore-installed -r "$PROJECT_ROOT_DIR/web_interface/requirements.txt"; then
         echo "✓ Web interface dependencies installed"
         # Create marker file to indicate dependencies are installed
         touch "$PROJECT_ROOT_DIR/.web_deps_installed"
@@ -977,7 +984,9 @@ else
     else
         echo "Using pip to install dependencies..."
         if [ -f "$PROJECT_ROOT_DIR/requirements_web_v2.txt" ]; then
-            python3 -m pip install --break-system-packages --prefer-binary -r requirements_web_v2.txt
+            # --ignore-installed: see the Step 5 web_interface/requirements.txt
+            # install above — same apt/pip RECORD-file conflict applies here.
+            python3 -m pip install --break-system-packages --prefer-binary --ignore-installed -r requirements_web_v2.txt
         else
             echo "⚠ requirements_web_v2.txt not found; skipping web dependency install"
         fi