Codex installation with the ChatGPT help

.gitignore

@@ -11,3 +11,5 @@ src/main/resources/trained_model
 bioformats*.*
 metadata*.*
 /bin/
+AGENTS.md
+run-codex.sh

INSTALL-CODEX-ECLIPSE.md

+# Codex + Eclipse Installation (Kubuntu 24.04)
+
+This document describes a known-working setup for using OpenAI Codex CLI
+alongside Eclipse on Kubuntu 24.04, with Codex launched from Eclipse in a real
+terminal (Konsole).
+
+## Prerequisites
+- Kubuntu 24.04
+- Eclipse (any recent version)
+- Git
+- Node.js + npm (user-level install, no sudo)
+- Konsole (default KDE terminal)
+
+## 1. Install Codex CLI (user-local)
+
+Do NOT use sudo.
+
+    npm install -g @openai/codex
+
+Verify:
+
+    which codex
+    codex --version
+
+The path should be under your home directory (for example ~/.npm-global/bin/codex).
+
+## 2. Authenticate Codex
+
+Run:
+
+    codex
+
+- Select “Sign in with ChatGPT” using the keyboard
+- Open the provided link in a normal Firefox window
+- Complete login
+- Exit Codex with Ctrl+D
+
+Authentication is stored locally; this is done once per machine.
+
+## 3. Create a launcher script in the repo
+
+In the root of your Git repository:
+
+    mkdir -p tools
+    cat > tools/run-codex.sh <<'EOF'
+    #!/usr/bin/env bash
+    exec /FULL/PATH/TO/codex
+    EOF
+    chmod +x tools/run-codex.sh
+
+Replace /FULL/PATH/TO/codex with the output of `which codex`
+(for example /home/elphel/.npm-global/bin/codex).
+
+This avoids PATH issues when launching from Eclipse.
+
+## 4. Configure Eclipse External Tool (Konsole)
+
+In Eclipse:
+
+Run → External Tools → External Tools Configurations…
+
+Create a new Program configuration.
+
+Main tab:
+- Name: Codex
+- Location: /usr/bin/konsole
+- Working Directory: Browse Workspace → select project root
+- Arguments:
+
+    --workdir "/absolute/path/to/your/project" -e bash -lc "./tools/run-codex.sh"
+
+(Common tab: enable “Display in favorites menu → External Tools”.)
+
+Apply and Run.
+
+A Konsole window should open and display the Codex UI.
+
+## 5. Add AGENTS.md (recommended)
+
+Create AGENTS.md in the repo root:
+
+    ## Build
+    - mvn -DskipTests clean package
+
+    ## Running
+    - Prefer Eclipse Run/Debug configurations.
+    - Do not invent CLI run commands.
+
+    ## Scope
+    - Make minimal, focused changes.
+    - Ask before touching GPU/CUDA code.
+
+Restart Codex after editing AGENTS.md.
+
+## Daily workflow
+
+1. Work in Eclipse
+2. Launch Codex via Run → External Tools → Codex
+3. Ask Codex to review or modify local code
+4. Review changes in Eclipse
+5. Commit and push
+
+## Notes
+- Codex requires a real terminal (TTY); always launch via Konsole
+- Eclipse internal console will not work
+- Codex rereads AGENTS.md on startup
+- No /reload command exists; restart Codex instead