diff --git a/hermes_cli/setup.py b/hermes_cli/setup.py
index a766e3afe..946021a2a 100644
--- a/hermes_cli/setup.py
+++ b/hermes_cli/setup.py
@@ -662,16 +662,11 @@ def run_setup_wizard(args):
     print()
     
     # Show file locations prominently
-    print(color("📁 Your configuration files:", Colors.CYAN, Colors.BOLD))
+    print(color("📁 All your files are in ~/.hermes/:", Colors.CYAN, Colors.BOLD))
     print()
     print(f"   {color('Settings:', Colors.YELLOW)}  {get_config_path()}")
-    print(f"              Model, terminal backend, compression, etc.")
-    print()
     print(f"   {color('API Keys:', Colors.YELLOW)}  {get_env_path()}")
-    print(f"              OpenRouter, Custom Endpoint, tool API keys")
-    print()
-    print(f"   {color('Data:', Colors.YELLOW)}      {hermes_home}/")
-    print(f"              Cron jobs, sessions, logs")
+    print(f"   {color('Data:', Colors.YELLOW)}      {hermes_home}/cron/, sessions/, logs/")
     print()
     
     print(color("─" * 60, Colors.DIM))
diff --git a/scripts/install.ps1 b/scripts/install.ps1
index 9cecb4582..caf80288d 100644
--- a/scripts/install.ps1
+++ b/scripts/install.ps1
@@ -15,7 +15,8 @@ param(
     [switch]$NoVenv,
     [switch]$SkipSetup,
     [string]$Branch = "main",
-    [string]$InstallDir = "$env:USERPROFILE\.hermes-agent"
+    [string]$HermesHome = "$env:USERPROFILE\.hermes",
+    [string]$InstallDir = "$env:USERPROFILE\.hermes\hermes-agent"
 )
 
 $ErrorActionPreference = "Stop"
@@ -248,36 +249,40 @@ function Set-PathVariable {
 function Copy-ConfigTemplates {
     Write-Info "Setting up configuration files..."
     
-    Push-Location $InstallDir
+    # Create ~/.hermes directory structure (config at top level, code in subdir)
+    New-Item -ItemType Directory -Force -Path "$HermesHome\cron" | Out-Null
+    New-Item -ItemType Directory -Force -Path "$HermesHome\sessions" | Out-Null
+    New-Item -ItemType Directory -Force -Path "$HermesHome\logs" | Out-Null
     
-    # Create .env from example
-    if (-not (Test-Path ".env")) {
-        if (Test-Path ".env.example") {
-            Copy-Item ".env.example" ".env"
-            Write-Success "Created .env from template"
+    # Create .env at ~/.hermes/.env (top level, easy to find)
+    $envPath = "$HermesHome\.env"
+    if (-not (Test-Path $envPath)) {
+        $examplePath = "$InstallDir\.env.example"
+        if (Test-Path $examplePath) {
+            Copy-Item $examplePath $envPath
+            Write-Success "Created ~/.hermes/.env from template"
+        } else {
+            # Create empty .env if no example exists
+            New-Item -ItemType File -Force -Path $envPath | Out-Null
+            Write-Success "Created ~/.hermes/.env"
         }
     } else {
-        Write-Info ".env already exists, keeping it"
+        Write-Info "~/.hermes/.env already exists, keeping it"
     }
     
-    # Create cli-config.yaml from example
-    if (-not (Test-Path "cli-config.yaml")) {
-        if (Test-Path "cli-config.yaml.example") {
-            Copy-Item "cli-config.yaml.example" "cli-config.yaml"
-            Write-Success "Created cli-config.yaml from template"
+    # Create config.yaml at ~/.hermes/config.yaml (top level, easy to find)
+    $configPath = "$HermesHome\config.yaml"
+    if (-not (Test-Path $configPath)) {
+        $examplePath = "$InstallDir\cli-config.yaml.example"
+        if (Test-Path $examplePath) {
+            Copy-Item $examplePath $configPath
+            Write-Success "Created ~/.hermes/config.yaml from template"
         }
     } else {
-        Write-Info "cli-config.yaml already exists, keeping it"
+        Write-Info "~/.hermes/config.yaml already exists, keeping it"
     }
     
-    Pop-Location
-    
-    # Create user data directory
-    $hermesDir = "$env:USERPROFILE\.hermes"
-    New-Item -ItemType Directory -Force -Path "$hermesDir\cron" | Out-Null
-    New-Item -ItemType Directory -Force -Path "$hermesDir\sessions" | Out-Null
-    New-Item -ItemType Directory -Force -Path "$hermesDir\logs" | Out-Null
-    Write-Success "Created ~/.hermes data directory"
+    Write-Success "Configuration directory ready: ~/.hermes/"
 }
 
 function Install-NodeDeps {
@@ -330,16 +335,16 @@ function Write-Completion {
     Write-Host ""
     
     # Show file locations
-    Write-Host "📁 Your files:" -ForegroundColor Cyan
+    Write-Host "📁 Your files (all in ~/.hermes/):" -ForegroundColor Cyan
     Write-Host ""
-    Write-Host "   Install:   " -NoNewline -ForegroundColor Yellow
-    Write-Host "$InstallDir"
     Write-Host "   Config:    " -NoNewline -ForegroundColor Yellow
-    Write-Host "$env:USERPROFILE\.hermes\config.yaml"
+    Write-Host "$HermesHome\config.yaml"
     Write-Host "   API Keys:  " -NoNewline -ForegroundColor Yellow
-    Write-Host "$env:USERPROFILE\.hermes\.env"
+    Write-Host "$HermesHome\.env"
     Write-Host "   Data:      " -NoNewline -ForegroundColor Yellow
-    Write-Host "$env:USERPROFILE\.hermes\ (cron, sessions, logs)"
+    Write-Host "$HermesHome\cron\, sessions\, logs\"
+    Write-Host "   Code:      " -NoNewline -ForegroundColor Yellow
+    Write-Host "$HermesHome\hermes-agent\"
     Write-Host ""
     
     Write-Host "─────────────────────────────────────────────────────────" -ForegroundColor Cyan
diff --git a/scripts/install.sh b/scripts/install.sh
index 69e283e56..463a0d5be 100755
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -27,7 +27,8 @@ BOLD='\033[1m'
 # Configuration
 REPO_URL_SSH="git@github.com:NousResearch/hermes-agent.git"
 REPO_URL_HTTPS="https://github.com/NousResearch/hermes-agent.git"
-INSTALL_DIR="${HERMES_INSTALL_DIR:-$HOME/.hermes-agent}"
+HERMES_HOME="$HOME/.hermes"
+INSTALL_DIR="${HERMES_INSTALL_DIR:-$HERMES_HOME/hermes-agent}"
 PYTHON_MIN_VERSION="3.10"
 
 # Options
@@ -401,31 +402,36 @@ EOF
 copy_config_templates() {
     log_info "Setting up configuration files..."
     
-    # Create .env from example
-    if [ ! -f "$INSTALL_DIR/.env" ]; then
+    # Create ~/.hermes directory structure (config at top level, code in subdir)
+    mkdir -p "$HERMES_HOME/cron"
+    mkdir -p "$HERMES_HOME/sessions"
+    mkdir -p "$HERMES_HOME/logs"
+    
+    # Create .env at ~/.hermes/.env (top level, easy to find)
+    if [ ! -f "$HERMES_HOME/.env" ]; then
         if [ -f "$INSTALL_DIR/.env.example" ]; then
-            cp "$INSTALL_DIR/.env.example" "$INSTALL_DIR/.env"
-            log_success "Created .env from template"
+            cp "$INSTALL_DIR/.env.example" "$HERMES_HOME/.env"
+            log_success "Created ~/.hermes/.env from template"
+        else
+            # Create empty .env if no example exists
+            touch "$HERMES_HOME/.env"
+            log_success "Created ~/.hermes/.env"
         fi
     else
-        log_info ".env already exists, keeping it"
+        log_info "~/.hermes/.env already exists, keeping it"
     fi
     
-    # Create cli-config.yaml from example
-    if [ ! -f "$INSTALL_DIR/cli-config.yaml" ]; then
+    # Create config.yaml at ~/.hermes/config.yaml (top level, easy to find)
+    if [ ! -f "$HERMES_HOME/config.yaml" ]; then
         if [ -f "$INSTALL_DIR/cli-config.yaml.example" ]; then
-            cp "$INSTALL_DIR/cli-config.yaml.example" "$INSTALL_DIR/cli-config.yaml"
-            log_success "Created cli-config.yaml from template"
+            cp "$INSTALL_DIR/cli-config.yaml.example" "$HERMES_HOME/config.yaml"
+            log_success "Created ~/.hermes/config.yaml from template"
         fi
     else
-        log_info "cli-config.yaml already exists, keeping it"
+        log_info "~/.hermes/config.yaml already exists, keeping it"
     fi
     
-    # Create ~/.hermes directory for user data
-    mkdir -p "$HOME/.hermes/cron"
-    mkdir -p "$HOME/.hermes/sessions"
-    mkdir -p "$HOME/.hermes/logs"
-    log_success "Created ~/.hermes data directory"
+    log_success "Configuration directory ready: ~/.hermes/"
 }
 
 install_node_deps() {
@@ -473,12 +479,12 @@ print_success() {
     echo ""
     
     # Show file locations
-    echo -e "${CYAN}${BOLD}📁 Your files:${NC}"
+    echo -e "${CYAN}${BOLD}📁 Your files (all in ~/.hermes/):${NC}"
     echo ""
-    echo -e "   ${YELLOW}Install:${NC}   $INSTALL_DIR"
     echo -e "   ${YELLOW}Config:${NC}    ~/.hermes/config.yaml"
     echo -e "   ${YELLOW}API Keys:${NC}  ~/.hermes/.env"
-    echo -e "   ${YELLOW}Data:${NC}      ~/.hermes/ (cron, sessions, logs)"
+    echo -e "   ${YELLOW}Data:${NC}      ~/.hermes/cron/, sessions/, logs/"
+    echo -e "   ${YELLOW}Code:${NC}      ~/.hermes/hermes-agent/"
     echo ""
     
     echo -e "${CYAN}─────────────────────────────────────────────────────────${NC}"