docs: clarify plugin paths and fix systemd manual install bug

PLUGIN_DEVELOPMENT_GUIDE.md
- Added a "Plugin directory note" callout near the top explaining
  the plugins/ vs plugin-repos/ split:
  - Dev workflow uses plugins/ (where dev_plugin_setup.sh creates
    symlinks)
  - Production / Plugin Store uses plugin-repos/ (the configurable
    default per config.template.json:130)
  - The plugin loader falls back to plugins/ so dev symlinks are
    picked up automatically (schema_manager.py:77)
  - User can set plugins_directory to "plugins" in the General tab
    if they want both to share a directory

CLAUDE.md
- The Project Structure section had plugins/ and plugin-repos/
  exactly reversed:
  - Old: "plugins/ - Installed plugins directory (gitignored)"
         "plugin-repos/ - Development symlinks to monorepo plugin dirs"
  - Real: plugin-repos/ is the canonical Plugin Store install
    location and is not gitignored. plugins/* IS gitignored
    (verified in .gitignore) and is the legacy/dev location used by
    scripts/dev/dev_plugin_setup.sh.
  Reversed the descriptions and added line refs.

systemd/README.md
- "Manual Installation" section told users to copy the unit file
  directly to /etc/systemd/system/. Verified the unit file in
  systemd/ledmatrix.service contains __PROJECT_ROOT_DIR__
  placeholders that the install scripts substitute at install time.
  A user following the manual steps would get a service that fails
  to start with "WorkingDirectory=__PROJECT_ROOT_DIR__" errors.
  Added a clear warning and a sed snippet that substitutes the
  placeholder before installing.

src/common/README.md
- Was missing 2 of the 11 utility modules in the directory
  (verified with ls): permission_utils.py and cli.py. Added brief
  descriptions for both.

Out-of-scope code bug found while auditing (flagged but not fixed):
- scripts/dev/dev_plugin_setup.sh:9 sets PROJECT_ROOT="$SCRIPT_DIR"
  which resolves to scripts/dev/, not the project root. This means
  the script's PLUGINS_DIR resolves to scripts/dev/plugins/ instead
  of the project's plugins/ — confirmed by the existence of
  scripts/dev/plugins/of-the-day/ from prior runs. Real fix is to
  set PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)". Not fixing in
  this docs PR.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

CLAUDE.md

@@ -4,8 +4,14 @@
 - `src/plugin_system/` — Plugin loader, manager, store manager, base plugin class
 - `web_interface/` — Flask web UI (blueprints, templates, static JS)
 - `config/config.json` — User plugin configuration (persists across plugin reinstalls)
-- `plugins/` — Installed plugins directory (gitignored)
-- `plugin-repos/` — Development symlinks to monorepo plugin dirs
+- `plugin-repos/` — **Default** plugin install directory used by the
+  Plugin Store, set by `plugin_system.plugins_directory` in
+  `config.json` (default per `config/config.template.json:130`).
+  Not gitignored.
+- `plugins/` — Legacy/dev plugin location. Gitignored (`plugins/*`).
+  Used by `scripts/dev/dev_plugin_setup.sh` for symlinks. The plugin
+  loader falls back to it when something isn't found in `plugin-repos/`
+  (`src/plugin_system/schema_manager.py:77`).
 
 ## Plugin System
 - Plugins inherit from `BasePlugin` in `src/plugin_system/base_plugin.py`

docs/PLUGIN_DEVELOPMENT_GUIDE.md

@@ -12,6 +12,15 @@ When developing plugins in separate repositories, you need a way to:
 
 The solution uses **symbolic links** to connect plugin repositories to the `plugins/` directory, combined with a helper script to manage the linking process.
 
+> **Plugin directory note:** the dev workflow described here puts
+> symlinks in `plugins/`. The plugin loader's *production* default is
+> `plugin-repos/` (set by `plugin_system.plugins_directory` in
+> `config.json`), but it falls back to `plugins/` so the dev symlinks
+> are picked up automatically. The Plugin Store installs to
+> `plugin-repos/`. If you want both your dev symlinks *and* store
+> installs to share the same directory, set `plugins_directory` to
+> `plugins` in the General tab of the web UI.
+
 ## Quick Start
 
 ### 1. Link a Plugin from GitHub

src/common/README.md

@@ -71,6 +71,17 @@ General-purpose utility functions:
 - Boolean parsing
 - Logger creation (deprecated - use `src.logging_config.get_logger()`)
 
+## Permission Utilities (`permission_utils.py`)
+
+Helpers for ensuring directory permissions and ownership are correct
+when running as a service (used by `CacheManager` to set up its
+persistent cache directory).
+
+## CLI Helpers (`cli.py`)
+
+Shared CLI argument parsing helpers used by `scripts/dev/*` and other
+command-line entry points.
+
 ## Best Practices
 
 1. **Use centralized logging**: Import from `src.logging_config` instead of creating loggers directly

systemd/README.md

@@ -28,14 +28,29 @@ These service files are installed by the installation scripts in `scripts/instal
 
 ## Manual Installation
 
-If you need to install a service manually:
-
-```bash
-sudo cp systemd/ledmatrix.service /etc/systemd/system/
-sudo systemctl daemon-reload
-sudo systemctl enable ledmatrix.service
-sudo systemctl start ledmatrix.service
-```
+> **Important:** the unit files in this directory contain
+> `__PROJECT_ROOT_DIR__` placeholders that the install scripts replace
+> with the actual project directory at install time. Do **not** copy
+> them directly to `/etc/systemd/system/` — the service will fail to
+> start with `WorkingDirectory=__PROJECT_ROOT_DIR__` errors.
+>
+> Always install via the helper script:
+>
+> ```bash
+> sudo ./scripts/install/install_service.sh
+> ```
+>
+> If you really need to do it by hand, substitute the placeholder
+> first:
+>
+> ```bash
+> PROJECT_ROOT="$(pwd)"
+> sed "s|__PROJECT_ROOT_DIR__|$PROJECT_ROOT|g" systemd/ledmatrix.service \
+>   | sudo tee /etc/systemd/system/ledmatrix.service > /dev/null
+> sudo systemctl daemon-reload
+> sudo systemctl enable ledmatrix.service
+> sudo systemctl start ledmatrix.service
+> ```
 
 ## Service Management