fix(codeprism-moth-specs): add --mcp flag to server args for proper MCP mode initialization

- Add --mcp flag to all comprehensive test specifications (python, java, rust, javascript)
- Add --mcp flag to all tool test specifications (core-navigation, flow-analysis, search-discovery, complexity-analysis, specialized-analysis)
- Add --mcp flag to workflow orchestration specification
- Fixes MCP connection error: 'Failed to create MCP service: connection closed: initialize response'
- Enables proper stdio transport communication between moth test harness and codeprism server

The codeprism binary requires the --mcp flag to start in MCP server mode.
Without this flag, it displays help text instead of starting the MCP protocol handler.

closes #[related to codeprism-moth-specs workflow failures]

Author: milliondreams

crates/codeprism-moth-specs/codeprism/comprehensive/codeprism-java-comprehensive.yaml

@@ -18,7 +18,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/comprehensive/codeprism-javascript-comprehensive.yaml

@@ -18,7 +18,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/comprehensive/codeprism-python-comprehensive.yaml

@@ -18,7 +18,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/comprehensive/codeprism-rust-comprehensive.yaml

@@ -18,7 +18,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/tools/codeprism-complexity-analysis.yaml

@@ -17,7 +17,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/tools/codeprism-core-navigation.yaml

@@ -17,7 +17,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/tools/codeprism-flow-analysis.yaml

@@ -17,7 +17,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/tools/codeprism-search-discovery.yaml

@@ -17,7 +17,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/tools/codeprism-specialized-analysis.yaml

@@ -17,7 +17,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

crates/codeprism-moth-specs/codeprism/workflows/codeprism-workflow-orchestration.yaml

@@ -17,7 +17,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"