Update RL tools and enhance configuration management

- Modified `model_tools.py` to update default model IDs and add new RL function `rl_test_inference`.
- Enhanced `README.md` with installation instructions for submodules and updated API key usage.
- Improved `rl_cli.py` to load configuration from `~/.hermes/config.yaml` and set terminal working directory for RL tools.
- Updated `run_agent.py` to handle empty string arguments as empty objects for better JSON validation.
- Refined installation scripts to ensure submodules are cloned and installed correctly, enhancing setup experience.

scripts/install.ps1

@@ -150,14 +150,15 @@ function Install-Repository {
         }
     } else {
         # Try SSH first (for private repo access), fall back to HTTPS
+        # Use --recurse-submodules to also clone mini-swe-agent and tinker-atropos
         Write-Info "Trying SSH clone..."
-        $sshResult = git clone --branch $Branch $RepoUrlSsh $InstallDir 2>&1
+        $sshResult = git clone --branch $Branch --recurse-submodules $RepoUrlSsh $InstallDir 2>&1
         
         if ($LASTEXITCODE -eq 0) {
             Write-Success "Cloned via SSH"
         } else {
             Write-Info "SSH failed, trying HTTPS..."
-            $httpsResult = git clone --branch $Branch $RepoUrlHttps $InstallDir 2>&1
+            $httpsResult = git clone --branch $Branch --recurse-submodules $RepoUrlHttps $InstallDir 2>&1
             
             if ($LASTEXITCODE -eq 0) {
                 Write-Success "Cloned via HTTPS"
@@ -171,6 +172,13 @@ function Install-Repository {
         }
     }
     
+    # Ensure submodules are initialized and updated (for existing installs or if --recurse failed)
+    Write-Info "Initializing submodules (mini-swe-agent, tinker-atropos)..."
+    Push-Location $InstallDir
+    git submodule update --init --recursive
+    Pop-Location
+    Write-Success "Submodules ready"
+    
     Write-Success "Repository ready"
 }
 
@@ -208,15 +216,43 @@ function Install-Dependencies {
         & .\venv\Scripts\Activate.ps1
     }
     
+    # Install main package
     try {
         pip install -e ".[all]" 2>&1 | Out-Null
     } catch {
         pip install -e "." | Out-Null
     }
     
+    Write-Success "Main package installed"
+    
+    # Install submodules
+    Write-Info "Installing mini-swe-agent (terminal tool backend)..."
+    if (Test-Path "mini-swe-agent\pyproject.toml") {
+        try {
+            pip install -e ".\mini-swe-agent" 2>&1 | Out-Null
+            Write-Success "mini-swe-agent installed"
+        } catch {
+            Write-Warning "mini-swe-agent install failed (terminal tools may not work)"
+        }
+    } else {
+        Write-Warning "mini-swe-agent not found (run: git submodule update --init)"
+    }
+    
+    Write-Info "Installing tinker-atropos (RL training backend)..."
+    if (Test-Path "tinker-atropos\pyproject.toml") {
+        try {
+            pip install -e ".\tinker-atropos" 2>&1 | Out-Null
+            Write-Success "tinker-atropos installed"
+        } catch {
+            Write-Warning "tinker-atropos install failed (RL tools may not work)"
+        }
+    } else {
+        Write-Warning "tinker-atropos not found (run: git submodule update --init)"
+    }
+    
     Pop-Location
     
-    Write-Success "Dependencies installed"
+    Write-Success "All dependencies installed"
 }
 
 function Set-PathVariable {

scripts/install.sh

@@ -292,12 +292,13 @@ clone_repo() {
         fi
     else
         # Try SSH first (for private repo access), fall back to HTTPS
+        # Use --recurse-submodules to also clone mini-swe-agent and tinker-atropos
         log_info "Trying SSH clone..."
-        if git clone --branch "$BRANCH" "$REPO_URL_SSH" "$INSTALL_DIR" 2>/dev/null; then
+        if git clone --branch "$BRANCH" --recurse-submodules "$REPO_URL_SSH" "$INSTALL_DIR" 2>/dev/null; then
             log_success "Cloned via SSH"
         else
             log_info "SSH failed, trying HTTPS..."
-            if git clone --branch "$BRANCH" "$REPO_URL_HTTPS" "$INSTALL_DIR"; then
+            if git clone --branch "$BRANCH" --recurse-submodules "$REPO_URL_HTTPS" "$INSTALL_DIR"; then
                 log_success "Cloned via HTTPS"
             else
                 log_error "Failed to clone repository"
@@ -310,6 +311,12 @@ clone_repo() {
     fi
     
     cd "$INSTALL_DIR"
+    
+    # Ensure submodules are initialized and updated (for existing installs or if --recurse failed)
+    log_info "Initializing submodules (mini-swe-agent, tinker-atropos)..."
+    git submodule update --init --recursive
+    log_success "Submodules ready"
+    
     log_success "Repository ready"
 }
 
@@ -343,10 +350,29 @@ install_deps() {
         source venv/bin/activate
     fi
     
-    # Install the package in editable mode with all extras
+    # Install the main package in editable mode with all extras
     pip install -e ".[all]" > /dev/null 2>&1 || pip install -e "." > /dev/null
     
-    log_success "Dependencies installed"
+    log_success "Main package installed"
+    
+    # Install submodules
+    log_info "Installing mini-swe-agent (terminal tool backend)..."
+    if [ -d "mini-swe-agent" ] && [ -f "mini-swe-agent/pyproject.toml" ]; then
+        pip install -e "./mini-swe-agent" > /dev/null 2>&1 || log_warn "mini-swe-agent install failed (terminal tools may not work)"
+        log_success "mini-swe-agent installed"
+    else
+        log_warn "mini-swe-agent not found (run: git submodule update --init)"
+    fi
+    
+    log_info "Installing tinker-atropos (RL training backend)..."
+    if [ -d "tinker-atropos" ] && [ -f "tinker-atropos/pyproject.toml" ]; then
+        pip install -e "./tinker-atropos" > /dev/null 2>&1 || log_warn "tinker-atropos install failed (RL tools may not work)"
+        log_success "tinker-atropos installed"
+    else
+        log_warn "tinker-atropos not found (run: git submodule update --init)"
+    fi
+    
+    log_success "All dependencies installed"
 }
 
 setup_path() {