software: Gitify node-red-dashboard (#573)

Configure node-red to use the git repository as `userDir` so that
changes to flows are visible in git.

Here is the output of `git status` after making changed in the node-red
editor:

![Screenshot From 2025-04-16
13-36-41](https://github.com/user-attachments/assets/a9f6b68f-1a04-44ff-84ce-0aa66bdc055d)

`settings.js` file was copied from
https://github.com/PlanktoScope/pallet-standard/blob/8fd23fded73b71d391d47a14ca79684cfcb6aeb7/packages/core/apps/planktoscope/node-red-dashboard/overlays/etc/nodered/settings.js

Previously the setting file was setup using forklift
https://github.com/PlanktoScope/pallet-standard/blob/8fd23fded73b71d391d47a14ca79684cfcb6aeb7/packages/core/apps/planktoscope/node-red-dashboard/overlays/etc/systemd/system/nodered.service.d/20-override.conf

This is "bypassing" forklift as I'm not familiar with it yet, it is
unclear if it will remain and in any case [dashboard
2](https://github.com/PlanktoScope/dashboard) will likely deprecate
this.


![image](https://github.com/user-attachments/assets/8437615a-a2b4-4a15-9905-ad74c086be6a)

Author: sonnyp

documentation/docs/community/contribute/tips-and-tricks.md

@@ -38,7 +38,7 @@ Make sure to replace `$planktoscope` with your PlanktoScope hostname, eg. `pksco
     <summary>On the PlanktoScope</summary>
 
 ```sh
-cd ~/Planktoscope
+cd ~/PlanktoScope
 # Enable Developer Mode
 ./software/distro/setup/planktoscope-app-env/PlanktoScope/enable-developer-mode
 # Configure git
@@ -54,7 +54,7 @@ git config --global user.name "Your Name"
 # Create an SSH key for the PlanktoScope specifically
 ssh-keygen -t ed25519 -C "pi@$planktoscope" -f ~/.ssh/$planktoscope
 # Make the SSH key accepted by the PlanktoScope
-scp ~/.ssh/$planktoscope.pub pkscope:~/.ssh/authorized_keys
+ssh-copy-id -i ~/.ssh/$planktoscope.pub pi@$planktoscope
 ```
 
 ```

software/distro/setup/planktoscope-app-env/PlanktoScope/enable-developer-mode

@@ -11,5 +11,3 @@ git fetch origin --filter=blob:none
 # "Resets the index but not the working tree (i.e., the changed files are preserved but not marked for commit) and reports what has not been updated."
 # https://git-scm.com/docs/git-reset#Documentation/git-reset.txt---mixed
 git reset --mixed $commit
-
-mkdir $HOME/.ssh

software/distro/setup/planktoscope-app-env/node-red-frontend/30-override.conf

@@ -0,0 +1,11 @@
+[Unit]
+# Start before mosquitto (provided via Forklift), to (hopefully) ensure that the Node-RED dashboard
+# is ready to catch all MQTT messages, such as messages sent by the Python backend right when it
+# starts (FIXME: make that unnecessary by allowing Node-RED to query the Python backend for any
+# information it needs later):
+Wants=forklift-apply.service
+Before=forklift-apply.service
+
+[Service]
+ExecStart=
+ExecStart=/usr/bin/env node-red-pi $NODE_OPTIONS --settings /home/pi/PlanktoScope/software/node-red-dashboard/settings.js $NODE_RED_OPTIONS

software/distro/setup/planktoscope-app-env/node-red-frontend/install.sh

@@ -3,7 +3,6 @@
 
 # Determine the base path for copied files
 config_files_root=$(dirname "$(realpath "$BASH_SOURCE")")
-distro_setup_files_root=$(dirname "$(dirname "$config_files_root")")
 
 # Get command-line args
 hardware_type="$1" # should be either adafruithat, planktoscopehat, fairscope-latest, or segmenter-only
@@ -36,7 +35,6 @@ sudo ln -s /run/machine-name /var/lib/planktoscope/machine-name
 # default, we do `pip3 install` as the pi user. This makes the smbus2 module available to Node-RED.
 # FIXME: get rid of the Node-RED nodes depending on smbus! That functionality should be moved into
 # the Python backend.
-# Note: for bookworm we need to install the apt package; for bullseye there is no apt package
 if ! sudo apt-get install -y python3-smbus2; then
   sudo apt-get install -y python3-pip
   pip3 install smbus2==0.4.3
@@ -47,15 +45,13 @@ fi
 curl -sL https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered |
   bash -s - --confirm-install --confirm-pi --no-init
 
-# Select the enabled dashboard
-mkdir -p "$HOME"/.node-red
-cp "$HOME/PlanktoScope/software/node-red-dashboard/flows/$hardware_type.json" \
-  "$HOME"/.node-red/flows.json
-mkdir -p "$HOME"/PlanktoScope
 cp "$HOME/PlanktoScope/software/node-red-dashboard/default-configs/$default_config.config.json" \
   "$HOME"/PlanktoScope/config.json
 
-# Install dependencies in a way that makes them available to Node-RED
-cp "$HOME"/PlanktoScope/software/node-red-dashboard/package.json "$HOME"/.node-red/
-cp "$HOME"/PlanktoScope/software/node-red-dashboard/package-lock.json "$HOME"/.node-red/
-npm --prefix "$HOME"/.node-red update
+# Configure node-red
+npm --prefix "$HOME"/PlanktoScope/software/node-red-dashboard install
+sudo mkdir -p /etc/systemd/system/nodered.service.d
+sudo cp $config_files_root/30-override.conf /etc/systemd/system/nodered.service.d/30-override.conf
+
+# Install dependencies to make them available to Node-RED
+npm --prefix "$HOME"/PlanktoScope/software/node-red-dashboard/$hardware_type install

software/node-red-dashboard/.gitignore

@@ -0,0 +1,2 @@
+*.backup
+.config.*.json