fix: add hermit cleanup to uvx and jbang scripts (#9616)

ui/desktop/src/bin/jbang

@@ -29,6 +29,34 @@ else
     RESOLVED_GOOSE_CONFIG_DIR="${HOME}/.config/goose"
 fi
 MCP_HERMIT_DIR="${RESOLVED_GOOSE_CONFIG_DIR}/mcp-hermit"
+mkdir -p "${RESOLVED_GOOSE_CONFIG_DIR}"
+HERMIT_SETUP_LOCK_DIR="${RESOLVED_GOOSE_CONFIG_DIR}/.mcp-hermit-setup.lock"
+HERMIT_SETUP_LOCK_TIMEOUT=300
+HERMIT_SETUP_LOCK_STARTED_AT=$(date +%s)
+while ! mkdir "${HERMIT_SETUP_LOCK_DIR}" 2>/dev/null; do
+    if [ $(( $(date +%s) - HERMIT_SETUP_LOCK_STARTED_AT )) -ge "${HERMIT_SETUP_LOCK_TIMEOUT}" ]; then
+        log "Timed out waiting for ${HERMIT_SETUP_LOCK_DIR}; removing stale lock."
+        rm -rf "${HERMIT_SETUP_LOCK_DIR}"
+        HERMIT_SETUP_LOCK_STARTED_AT=$(date +%s)
+    fi
+    sleep 0.1
+done
+trap 'rm -rf "${HERMIT_SETUP_LOCK_DIR}"; log "An error occurred. Exiting with status $?."' ERR
+trap 'rm -rf "${HERMIT_SETUP_LOCK_DIR}"' EXIT
+
+# One-time cleanup for existing Linux users to fix locking issues
+CLEANUP_MARKER="${RESOLVED_GOOSE_CONFIG_DIR}/.mcp-hermit-cleanup-v1"
+if [[ "$(uname -s)" == "Linux" ]] && [ ! -f "${CLEANUP_MARKER}" ]; then
+    log "Performing one-time cleanup of old mcp-hermit directory to fix locking issues."
+    if [ -d "${MCP_HERMIT_DIR}" ]; then
+        STALE_MCP_HERMIT_DIR="${MCP_HERMIT_DIR}.stale.$$"
+        mv "${MCP_HERMIT_DIR}" "${STALE_MCP_HERMIT_DIR}"
+        rm -rf "${STALE_MCP_HERMIT_DIR}"
+        log "Removed old mcp-hermit directory."
+    fi
+    touch "${CLEANUP_MARKER}"
+    log "Cleanup completed. Marker file created."
+fi
 
 # Ensure mcp-hermit/bin exists
 log "Creating directory ${MCP_HERMIT_DIR}/bin if it does not exist."
@@ -56,9 +84,41 @@ export HERMIT_STATE_DIR="${MCP_HERMIT_DIR}/cache"
 export PATH="${MCP_HERMIT_DIR}/bin:${PATH}"
 log "Updated PATH to include ${MCP_HERMIT_DIR}/bin."
 
-# Initialize hermit
-log "Initializing hermit."
-hermit init >> "$LOG_FILE"
+# Check if hermit environment is already initialized (only run init on first setup)
+if [ ! -f "bin/activate-hermit" ]; then
+    log "Hermit environment not yet initialized. Setting up hermit."
+
+    # Fix hermit self-update lock issues on Linux by using temp binary for init only
+    if [[ "$(uname -s)" == "Linux" ]]; then
+        log "Creating temp dir with bin subdirectory for hermit copy to avoid self-update locks."
+        HERMIT_TMP_DIR="/tmp/hermit_tmp_$$/bin"
+        mkdir -p "${HERMIT_TMP_DIR}"
+        cp "${MCP_HERMIT_DIR}/bin/hermit" "${HERMIT_TMP_DIR}/hermit"
+        chmod +x "${HERMIT_TMP_DIR}/hermit"
+        HERMIT_ORIGINAL_PATH="${PATH}"
+        export PATH="${HERMIT_TMP_DIR}:${PATH}"
+        HERMIT_CLEANUP_DIR="/tmp/hermit_tmp_$$"
+    fi
+
+    # Initialize hermit
+    log "Initializing hermit."
+    hermit init >> "$LOG_FILE"
+
+    # Clean up temp dir if it was created
+    if [[ -n "${HERMIT_CLEANUP_DIR:-}" ]]; then
+        log "Cleaning up temporary hermit binary directory."
+        export PATH="${HERMIT_ORIGINAL_PATH}"
+        rm -rf "${HERMIT_CLEANUP_DIR}"
+    fi
+else
+    log "Hermit environment already initialized. Skipping init."
+fi
+
+# Activate the environment with output redirected to log
+if [[ "$(uname -s)" == "Linux" ]]; then
+    log "Activating hermit environment."
+    { . "bin/activate-hermit"; } >> "$LOG_FILE" 2>&1
+fi
 
 # Install OpenJDK using hermit
 log "Installing OpenJDK with hermit."
@@ -77,6 +137,10 @@ log "hermit: $(which hermit)"
 log "java: $(which java)"
 log "jbang: $(which jbang)"
 
+rm -rf "${HERMIT_SETUP_LOCK_DIR}"
+trap 'log "An error occurred. Exiting with status $?."' ERR
+trap - EXIT
+
 # Check for custom registry settings
 log "Checking for GOOSE_JBANG_REGISTRY environment variable for custom jbang registry setup..."
 if [ -n "${GOOSE_JBANG_REGISTRY:-}" ] && curl -s --head --fail "$GOOSE_JBANG_REGISTRY" > /dev/null; then

ui/desktop/src/bin/node-setup-common.sh

@@ -32,16 +32,31 @@ else
     RESOLVED_GOOSE_CONFIG_DIR="${HOME}/.config/goose"
 fi
 MCP_HERMIT_DIR="${RESOLVED_GOOSE_CONFIG_DIR}/mcp-hermit"
+mkdir -p "${RESOLVED_GOOSE_CONFIG_DIR}"
+HERMIT_SETUP_LOCK_DIR="${RESOLVED_GOOSE_CONFIG_DIR}/.mcp-hermit-setup.lock"
+HERMIT_SETUP_LOCK_TIMEOUT=300
+HERMIT_SETUP_LOCK_STARTED_AT=$(date +%s)
+while ! mkdir "${HERMIT_SETUP_LOCK_DIR}" 2>/dev/null; do
+    if [ $(( $(date +%s) - HERMIT_SETUP_LOCK_STARTED_AT )) -ge "${HERMIT_SETUP_LOCK_TIMEOUT}" ]; then
+        log "Timed out waiting for ${HERMIT_SETUP_LOCK_DIR}; removing stale lock."
+        rm -rf "${HERMIT_SETUP_LOCK_DIR}"
+        HERMIT_SETUP_LOCK_STARTED_AT=$(date +%s)
+    fi
+    sleep 0.1
+done
+trap 'rm -rf "${HERMIT_SETUP_LOCK_DIR}"; log "An error occurred. Exiting with status $?."' ERR
+trap 'rm -rf "${HERMIT_SETUP_LOCK_DIR}"' EXIT
 
 # One-time cleanup for existing Linux users to fix locking issues
 CLEANUP_MARKER="${RESOLVED_GOOSE_CONFIG_DIR}/.mcp-hermit-cleanup-v1"
 if [[ "$(uname -s)" == "Linux" ]] && [ ! -f "${CLEANUP_MARKER}" ]; then
     log "Performing one-time cleanup of old mcp-hermit directory to fix locking issues."
     if [ -d "${MCP_HERMIT_DIR}" ]; then
-        rm -rf "${MCP_HERMIT_DIR}"
+        STALE_MCP_HERMIT_DIR="${MCP_HERMIT_DIR}.stale.$$"
+        mv "${MCP_HERMIT_DIR}" "${STALE_MCP_HERMIT_DIR}"
+        rm -rf "${STALE_MCP_HERMIT_DIR}"
         log "Removed old mcp-hermit directory."
     fi
-    mkdir -p "${RESOLVED_GOOSE_CONFIG_DIR}"
     touch "${CLEANUP_MARKER}"
     log "Cleanup completed. Marker file created."
 fi
@@ -91,6 +106,7 @@ if [ ! -f "bin/activate-hermit" ]; then
         mkdir -p "${HERMIT_TMP_DIR}"
         cp "${MCP_HERMIT_DIR}/bin/hermit" "${HERMIT_TMP_DIR}/hermit"
         chmod +x "${HERMIT_TMP_DIR}/hermit"
+        HERMIT_ORIGINAL_PATH="${PATH}"
         export PATH="${HERMIT_TMP_DIR}:${PATH}"
         HERMIT_CLEANUP_DIR="/tmp/hermit_tmp_$$"
     fi
@@ -102,6 +118,7 @@ if [ ! -f "bin/activate-hermit" ]; then
     # Clean up temp dir if it was created
     if [[ -n "${HERMIT_CLEANUP_DIR:-}" ]]; then
         log "Cleaning up temporary hermit binary directory."
+        export PATH="${HERMIT_ORIGINAL_PATH}"
         rm -rf "${HERMIT_CLEANUP_DIR}"
     fi
 else
@@ -124,6 +141,10 @@ log "hermit: $(which hermit)"
 log "node: $(which node)"
 log "npx: $(which npx)"
 
+rm -rf "${HERMIT_SETUP_LOCK_DIR}"
+trap 'log "An error occurred. Exiting with status $?."' ERR
+trap - EXIT
+
 
 log "Checking for GOOSE_NPM_REGISTRY and GOOSE_NPM_CERT environment variables for custom npm registry setup..."
 # Check if GOOSE_NPM_REGISTRY is set and accessible

ui/desktop/src/bin/uvx

@@ -29,6 +29,34 @@ else
     RESOLVED_GOOSE_CONFIG_DIR="${HOME}/.config/goose"
 fi
 MCP_HERMIT_DIR="${RESOLVED_GOOSE_CONFIG_DIR}/mcp-hermit"
+mkdir -p "${RESOLVED_GOOSE_CONFIG_DIR}"
+HERMIT_SETUP_LOCK_DIR="${RESOLVED_GOOSE_CONFIG_DIR}/.mcp-hermit-setup.lock"
+HERMIT_SETUP_LOCK_TIMEOUT=300
+HERMIT_SETUP_LOCK_STARTED_AT=$(date +%s)
+while ! mkdir "${HERMIT_SETUP_LOCK_DIR}" 2>/dev/null; do
+    if [ $(( $(date +%s) - HERMIT_SETUP_LOCK_STARTED_AT )) -ge "${HERMIT_SETUP_LOCK_TIMEOUT}" ]; then
+        log "Timed out waiting for ${HERMIT_SETUP_LOCK_DIR}; removing stale lock."
+        rm -rf "${HERMIT_SETUP_LOCK_DIR}"
+        HERMIT_SETUP_LOCK_STARTED_AT=$(date +%s)
+    fi
+    sleep 0.1
+done
+trap 'rm -rf "${HERMIT_SETUP_LOCK_DIR}"; log "An error occurred. Exiting with status $?."' ERR
+trap 'rm -rf "${HERMIT_SETUP_LOCK_DIR}"' EXIT
+
+# One-time cleanup for existing Linux users to fix locking issues
+CLEANUP_MARKER="${RESOLVED_GOOSE_CONFIG_DIR}/.mcp-hermit-cleanup-v1"
+if [[ "$(uname -s)" == "Linux" ]] && [ ! -f "${CLEANUP_MARKER}" ]; then
+    log "Performing one-time cleanup of old mcp-hermit directory to fix locking issues."
+    if [ -d "${MCP_HERMIT_DIR}" ]; then
+        STALE_MCP_HERMIT_DIR="${MCP_HERMIT_DIR}.stale.$$"
+        mv "${MCP_HERMIT_DIR}" "${STALE_MCP_HERMIT_DIR}"
+        rm -rf "${STALE_MCP_HERMIT_DIR}"
+        log "Removed old mcp-hermit directory."
+    fi
+    touch "${CLEANUP_MARKER}"
+    log "Cleanup completed. Marker file created."
+fi
 
 # Ensure mcp-hermit/bin exists
 log "Creating directory ${MCP_HERMIT_DIR}/bin if it does not exist."
@@ -62,9 +90,41 @@ log "Updated PATH to include ${MCP_HERMIT_DIR}/bin."
 log "Checking for hermit in PATH."
 which hermit >> "$LOG_FILE"
 
-# Initialize hermit
-log "Initializing hermit."
-hermit init >> "$LOG_FILE"
+# Check if hermit environment is already initialized (only run init on first setup)
+if [ ! -f "bin/activate-hermit" ]; then
+    log "Hermit environment not yet initialized. Setting up hermit."
+
+    # Fix hermit self-update lock issues on Linux by using temp binary for init only
+    if [[ "$(uname -s)" == "Linux" ]]; then
+        log "Creating temp dir with bin subdirectory for hermit copy to avoid self-update locks."
+        HERMIT_TMP_DIR="/tmp/hermit_tmp_$$/bin"
+        mkdir -p "${HERMIT_TMP_DIR}"
+        cp "${MCP_HERMIT_DIR}/bin/hermit" "${HERMIT_TMP_DIR}/hermit"
+        chmod +x "${HERMIT_TMP_DIR}/hermit"
+        HERMIT_ORIGINAL_PATH="${PATH}"
+        export PATH="${HERMIT_TMP_DIR}:${PATH}"
+        HERMIT_CLEANUP_DIR="/tmp/hermit_tmp_$$"
+    fi
+
+    # Initialize hermit
+    log "Initializing hermit."
+    hermit init >> "$LOG_FILE"
+
+    # Clean up temp dir if it was created
+    if [[ -n "${HERMIT_CLEANUP_DIR:-}" ]]; then
+        log "Cleaning up temporary hermit binary directory."
+        export PATH="${HERMIT_ORIGINAL_PATH}"
+        rm -rf "${HERMIT_CLEANUP_DIR}"
+    fi
+else
+    log "Hermit environment already initialized. Skipping init."
+fi
+
+# Activate the environment with output redirected to log
+if [[ "$(uname -s)" == "Linux" ]]; then
+    log "Activating hermit environment."
+    { . "bin/activate-hermit"; } >> "$LOG_FILE" 2>&1
+fi
 
 # Initialize python >= 3.10
 log "hermit install python 3.10"
@@ -80,6 +140,10 @@ log "hermit: $(which hermit)"
 log "uv: $(which uv)"
 log "uvx: $(which uvx)"
 
+rm -rf "${HERMIT_SETUP_LOCK_DIR}"
+trap 'log "An error occurred. Exiting with status $?."' ERR
+trap - EXIT
+
 
 log "Checking for GOOSE_UV_REGISTRY environment variable for custom python/pip/UV registry setup..."
 # Check if GOOSE_UV_REGISTRY is set and accessible