Merge pull request 'bug/mcp-env-vars-support' (#61) from bug/mcp-env-vars-support into master

Reviewed-on: #61

CLAUDE.md

@@ -57,6 +57,9 @@ cargo clippy --manifest-path src-tauri/Cargo.toml -- -D warnings
 
 # Rust quick type check (no linking)
 cargo check --manifest-path src-tauri/Cargo.toml
+
+# Frontend linting
+npx eslint . --max-warnings 0
 ```
 
 ### System Prerequisites (Linux/Fedora)
@@ -116,6 +119,8 @@ All command handlers receive `State<'_, AppState>` as a Tauri-injected parameter
 
 **Database encryption**: `cfg!(debug_assertions)` → plain SQLite; release → SQLCipher AES-256. Key from `TFTSR_DB_KEY` env var (defaults to a dev placeholder). DB path from `TFTSR_DATA_DIR` or platform data dir.
 
+**Credential encryption**: API keys stored in `AppSettings` are encrypted using AES-256-GCM via the `aes-gcm` crate. The encryption key is derived from `TFTSR_ENCRYPTION_KEY` env var. Credentials are encrypted on save and decrypted on load. See `commands/system.rs::save_settings()` for implementation.
+
 ### Frontend (React / TypeScript)
 
 **IPC layer**: All Tauri `invoke()` calls are in `src/lib/tauriCommands.ts`. Every command has a typed wrapper function (e.g., `createIssueCmd`, `chatMessageCmd`). This is the single source of truth for the frontend's API surface.

README.md

@@ -325,7 +325,3 @@ Override with the `TFTSR_DATA_DIR` environment variable.
 | 12 | Release Packaging | ✅ linux/amd64 · linux/arm64 (native) · windows/amd64 |
 
 ---
-
-## License
-
-Private — internal tooling. All rights reserved.

src-tauri/src/db/migrations.rs

@@ -283,6 +283,10 @@ pub fn run_migrations(conn: &Connection) -> anyhow::Result<()> {
                 FROM image_attachments ia
                 JOIN issues i ON i.id = ia.issue_id;",
         ),
+        (
+            "023_add_mcp_env_config",
+            "ALTER TABLE mcp_servers ADD COLUMN env_config TEXT",
+        ),
     ];
 
     for (name, sql) in migrations {
@@ -1233,4 +1237,39 @@ mod tests {
             assert_eq!(count, 1, "{migration} should be recorded exactly once");
         }
     }
+
+    // ─── Migration 023: MCP env_config ──────────────────────────────────────────
+
+    #[test]
+    fn test_023_mcp_env_config_column() {
+        let conn = setup_test_db();
+
+        let mut stmt = conn.prepare("PRAGMA table_info(mcp_servers)").unwrap();
+        let columns: Vec<String> = stmt
+            .query_map([], |row| row.get::<_, String>(1))
+            .unwrap()
+            .collect::<Result<Vec<_>, _>>()
+            .unwrap();
+
+        assert!(
+            columns.contains(&"env_config".to_string()),
+            "mcp_servers table should have env_config column after migration 023"
+        );
+    }
+
+    #[test]
+    fn test_023_idempotent() {
+        let conn = Connection::open_in_memory().unwrap();
+        run_migrations(&conn).unwrap();
+        run_migrations(&conn).unwrap();
+
+        let applied: i64 = conn
+            .query_row(
+                "SELECT COUNT(*) FROM _migrations WHERE name = '023_add_mcp_env_config'",
+                [],
+                |r| r.get(0),
+            )
+            .unwrap();
+        assert_eq!(applied, 1, "023 should only be recorded once");
+    }
 }

src-tauri/src/mcp/client.rs

@@ -7,17 +7,26 @@ use crate::mcp::models::{McpResource, McpTool};
 /// Live connection to an MCP server.
 pub type McpConnection = RunningService<RoleClient, ()>;
 
-/// Connect to a stdio MCP server.
+/// Connect to a stdio MCP server with optional environment variables.
-pub async fn connect_stdio(command: &str, args: &[String]) -> Result<McpConnection, String> {
+pub async fn connect_stdio(
-    let transport = crate::mcp::transport::stdio::build_stdio_transport(command, args)?;
+    command: &str,
+    args: &[String],
+    env: std::collections::HashMap<String, String>,
+) -> Result<McpConnection, String> {
+    let transport = crate::mcp::transport::stdio::build_stdio_transport(command, args, env)?;
     ().serve(transport)
         .await
         .map_err(|e| format!("MCP stdio connection failed: {e}"))
 }
 
-/// Connect to an HTTP MCP server.
+/// Connect to an HTTP MCP server with optional custom headers.
-pub async fn connect_http(url: &str, auth_header: Option<&str>) -> Result<McpConnection, String> {
+pub async fn connect_http(
-    let transport = crate::mcp::transport::http::build_http_transport(url, auth_header);
+    url: &str,
+    auth_header: Option<&str>,
+    custom_headers: std::collections::HashMap<String, String>,
+) -> Result<McpConnection, String> {
+    let transport =
+        crate::mcp::transport::http::build_http_transport(url, auth_header, custom_headers);
     ().serve(transport)
         .await
         .map_err(|e| format!("MCP HTTP connection failed: {e}"))

src-tauri/src/mcp/discovery.rs

@@ -5,7 +5,8 @@ use tracing::{info, warn};
 use crate::mcp::client::{connect_http, connect_stdio, list_resources, list_tools, McpConnection};
 use crate::mcp::models::McpServer;
 use crate::mcp::store::{
-    get_server_auth_value, list_servers, replace_resources, replace_tools, update_discovery_status,
+    get_server_auth_value, get_server_env_config, list_servers, replace_resources, replace_tools,
+    update_discovery_status,
 };
 
 /// Discover a single MCP server: connect, list tools/resources, persist.
@@ -55,11 +56,49 @@ async fn discover_server_inner(
                         .collect()
                 })
                 .unwrap_or_default();
-            connect_stdio(command, &args).await?
+
+            // Parse plaintext env vars from transport_config.env
+            let plaintext_env: std::collections::HashMap<String, String> = config
+                .get("env")
+                .and_then(|v| v.as_object())
+                .map(|obj| {
+                    obj.iter()
+                        .filter_map(|(k, v)| v.as_str().map(|s| (k.clone(), s.to_string())))
+                        .collect()
+                })
+                .unwrap_or_default();
+
+            // Decrypt and parse encrypted env vars from env_config column
+            let encrypted_env = {
+                let db = state.db.lock().map_err(|e| e.to_string())?;
+                get_server_env_config(&db, &server.id)?
+            };
+
+            // Merge env vars (encrypted takes precedence over plaintext)
+            let mut merged_env = plaintext_env;
+            if let Some(enc_env) = encrypted_env {
+                merged_env.extend(enc_env);
+            }
+
+            connect_stdio(command, &args, merged_env).await?
         }
         "http" => {
             let auth_header = auth_value.as_deref();
-            connect_http(&server.url, auth_header).await?
+
+            // Parse custom headers from transport_config.headers
+            let config: serde_json::Value =
+                serde_json::from_str(&server.transport_config).unwrap_or_default();
+            let custom_headers: std::collections::HashMap<String, String> = config
+                .get("headers")
+                .and_then(|v| v.as_object())
+                .map(|obj| {
+                    obj.iter()
+                        .filter_map(|(k, v)| v.as_str().map(|s| (k.clone(), s.to_string())))
+                        .collect()
+                })
+                .unwrap_or_default();
+
+            connect_http(&server.url, auth_header, custom_headers).await?
         }
         other => return Err(format!("Unknown transport type: {other}")),
     };

src-tauri/src/mcp/models.rs

@@ -18,6 +18,8 @@ pub struct McpServer {
     pub discovery_error: Option<String>,
     pub created_at: String,
     pub updated_at: String,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub env_config: Option<String>,
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize)]
@@ -64,6 +66,8 @@ pub struct CreateMcpServerRequest {
     #[serde(skip_serializing_if = "Option::is_none")]
     pub auth_value: Option<String>,
     pub enabled: bool,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub env_config: Option<String>,
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize)]
@@ -82,4 +86,6 @@ pub struct UpdateMcpServerRequest {
     pub auth_value: Option<String>,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub enabled: Option<bool>,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub env_config: Option<String>,
 }

src-tauri/src/mcp/store.rs

@@ -15,10 +15,15 @@ pub fn create_server(conn: &Connection, req: &CreateMcpServerRequest) -> Result<
         _ => None,
     };
 
+    let encrypted_env = match &req.env_config {
+        Some(env_json) if !env_json.trim().is_empty() => Some(encrypt_token(env_json)?),
+        _ => None,
+    };
+
     conn.execute(
         "INSERT INTO mcp_servers
-            (id, name, url, transport_type, transport_config, auth_type, auth_value, enabled, created_at, updated_at)
+            (id, name, url, transport_type, transport_config, auth_type, auth_value, enabled, env_config, created_at, updated_at)
-         VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7, ?8, ?9, ?9)",
+         VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7, ?8, ?9, ?10, ?10)",
         rusqlite::params![
             id,
             req.name,
@@ -28,6 +33,7 @@ pub fn create_server(conn: &Connection, req: &CreateMcpServerRequest) -> Result<
             req.auth_type,
             encrypted_auth,
             req.enabled as i32,
+            encrypted_env,
             now,
         ],
     )
@@ -41,7 +47,7 @@ pub fn get_server(conn: &Connection, id: &str) -> Result<Option<McpServer>, Stri
         .query_row(
             "SELECT id, name, url, transport_type, transport_config, auth_type, auth_value,
                     enabled, last_discovered_at, discovery_status, discovery_error,
-                    created_at, updated_at
+                    created_at, updated_at, env_config
              FROM mcp_servers WHERE id = ?1",
             [id],
             |row| {
@@ -59,6 +65,7 @@ pub fn get_server(conn: &Connection, id: &str) -> Result<Option<McpServer>, Stri
                     discovery_error: row.get(10)?,
                     created_at: row.get(11)?,
                     updated_at: row.get(12)?,
+                    env_config: row.get(13)?,
                 })
             },
         )
@@ -72,7 +79,7 @@ pub fn list_servers(conn: &Connection) -> Result<Vec<McpServer>, String> {
         .prepare(
             "SELECT id, name, url, transport_type, transport_config, auth_type, auth_value,
                     enabled, last_discovered_at, discovery_status, discovery_error,
-                    created_at, updated_at
+                    created_at, updated_at, env_config
              FROM mcp_servers ORDER BY created_at ASC",
         )
         .map_err(|e| e.to_string())?;
@@ -93,6 +100,7 @@ pub fn list_servers(conn: &Connection) -> Result<Vec<McpServer>, String> {
                 discovery_error: row.get(10)?,
                 created_at: row.get(11)?,
                 updated_at: row.get(12)?,
+                env_config: row.get(13)?,
             })
         })
         .map_err(|e| e.to_string())?
@@ -116,11 +124,17 @@ pub fn update_server(
         None => existing.auth_value.clone(),
     };
 
+    let new_encrypted_env = match &req.env_config {
+        Some(env_json) if !env_json.trim().is_empty() => Some(encrypt_token(env_json)?),
+        Some(_) => None,                     // Empty string = clear env_config
+        None => existing.env_config.clone(), // No update requested
+    };
+
     conn.execute(
         "UPDATE mcp_servers SET
             name = ?1, url = ?2, transport_type = ?3, transport_config = ?4,
-            auth_type = ?5, auth_value = ?6, enabled = ?7, updated_at = ?8
+            auth_type = ?5, auth_value = ?6, enabled = ?7, env_config = ?8, updated_at = ?9
-         WHERE id = ?9",
+         WHERE id = ?10",
         rusqlite::params![
             req.name.as_deref().unwrap_or(&existing.name),
             req.url.as_deref().unwrap_or(&existing.url),
@@ -135,6 +149,7 @@ pub fn update_server(
             req.enabled
                 .map(|b| b as i32)
                 .unwrap_or(existing.enabled as i32),
+            new_encrypted_env,
             now,
             id,
         ],
@@ -308,6 +323,34 @@ pub fn get_resource_count(conn: &Connection, server_id: &str) -> Result<usize, S
     .map_err(|e| e.to_string())
 }
 
+/// Decrypt and parse env_config from database, returning a HashMap.
+/// Returns None if env_config is NULL, or an error if decryption/parsing fails.
+pub fn get_server_env_config(
+    conn: &Connection,
+    server_id: &str,
+) -> Result<Option<std::collections::HashMap<String, String>>, String> {
+    let encrypted: Option<String> = conn
+        .query_row(
+            "SELECT env_config FROM mcp_servers WHERE id = ?1",
+            [server_id],
+            |row| row.get(0),
+        )
+        .optional()
+        .map_err(|e| e.to_string())?
+        .flatten();
+
+    match encrypted {
+        Some(enc) => {
+            let decrypted = decrypt_token(&enc)?;
+            let parsed: std::collections::HashMap<String, String> =
+                serde_json::from_str(&decrypted)
+                    .map_err(|e| format!("Failed to parse env_config JSON: {e}"))?;
+            Ok(Some(parsed))
+        }
+        None => Ok(None),
+    }
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -328,6 +371,7 @@ mod tests {
             auth_type: "none".to_string(),
             auth_value: None,
             enabled: true,
+            env_config: None,
         }
     }
 
@@ -362,6 +406,7 @@ mod tests {
                 auth_type: None,
                 auth_value: None,
                 enabled: None,
+                env_config: None,
             },
         )
         .unwrap();
@@ -385,6 +430,7 @@ mod tests {
             auth_type: "bearer".to_string(),
             auth_value: Some("super-secret-token".to_string()),
             enabled: true,
+            env_config: None,
         };
         let server = create_server(&conn, &req).unwrap();
 
@@ -479,4 +525,127 @@ mod tests {
             .unwrap();
         assert_eq!(count, 0, "cascade delete should clear mcp_tools");
     }
+
+    #[test]
+    fn test_env_config_encrypted_at_rest() {
+        let conn = setup();
+
+        let req = CreateMcpServerRequest {
+            name: "Env Test".to_string(),
+            url: "".to_string(),
+            transport_type: "stdio".to_string(),
+            transport_config: r#"{"command":"/usr/bin/test","args":[]}"#.to_string(),
+            auth_type: "none".to_string(),
+            auth_value: None,
+            enabled: true,
+            env_config: Some(r#"{"API_KEY":"secret123","DEBUG":"1"}"#.to_string()),
+        };
+        let server = create_server(&conn, &req).unwrap();
+
+        // Raw DB value must be encrypted (not equal to plaintext)
+        let raw: Option<String> = conn
+            .query_row(
+                "SELECT env_config FROM mcp_servers WHERE id = ?1",
+                [&server.id],
+                |r| r.get(0),
+            )
+            .unwrap();
+        let raw = raw.unwrap();
+        assert_ne!(
+            raw, r#"{"API_KEY":"secret123","DEBUG":"1"}"#,
+            "env_config should be encrypted at rest"
+        );
+
+        // Decrypted value must match original
+        let env_map = get_server_env_config(&conn, &server.id).unwrap().unwrap();
+        assert_eq!(env_map.get("API_KEY").unwrap(), "secret123");
+        assert_eq!(env_map.get("DEBUG").unwrap(), "1");
+    }
+
+    #[test]
+    fn test_update_env_config() {
+        let conn = setup();
+
+        let server = create_server(&conn, &make_req("Env Update")).unwrap();
+        assert!(server.env_config.is_none());
+
+        let updated = update_server(
+            &conn,
+            &server.id,
+            &UpdateMcpServerRequest {
+                name: None,
+                url: None,
+                transport_type: None,
+                transport_config: None,
+                auth_type: None,
+                auth_value: None,
+                enabled: None,
+                env_config: Some(r#"{"NEW_VAR":"value"}"#.to_string()),
+            },
+        )
+        .unwrap();
+
+        assert!(updated.env_config.is_some());
+        let env_map = get_server_env_config(&conn, &server.id).unwrap().unwrap();
+        assert_eq!(env_map.get("NEW_VAR").unwrap(), "value");
+    }
+
+    #[test]
+    fn test_clear_env_config_with_empty_string() {
+        let conn = setup();
+
+        let mut req = make_req("Clear Env");
+        req.env_config = Some(r#"{"KEY":"val"}"#.to_string());
+        let server = create_server(&conn, &req).unwrap();
+        assert!(server.env_config.is_some());
+
+        let updated = update_server(
+            &conn,
+            &server.id,
+            &UpdateMcpServerRequest {
+                name: None,
+                url: None,
+                transport_type: None,
+                transport_config: None,
+                auth_type: None,
+                auth_value: None,
+                enabled: None,
+                env_config: Some("".to_string()), // Clear
+            },
+        )
+        .unwrap();
+
+        assert!(updated.env_config.is_none());
+    }
+
+    #[test]
+    fn test_env_config_none_preserves_existing() {
+        let conn = setup();
+
+        let mut req = make_req("Preserve Env");
+        req.env_config = Some(r#"{"ORIGINAL":"value"}"#.to_string());
+        let server = create_server(&conn, &req).unwrap();
+
+        // Update without touching env_config
+        let updated = update_server(
+            &conn,
+            &server.id,
+            &UpdateMcpServerRequest {
+                name: Some("New Name".to_string()),
+                url: None,
+                transport_type: None,
+                transport_config: None,
+                auth_type: None,
+                auth_value: None,
+                enabled: None,
+                env_config: None, // Don't update
+            },
+        )
+        .unwrap();
+
+        // env_config should still be there
+        assert!(updated.env_config.is_some());
+        let env_map = get_server_env_config(&conn, &server.id).unwrap().unwrap();
+        assert_eq!(env_map.get("ORIGINAL").unwrap(), "value");
+    }
 }

src-tauri/src/mcp/transport/http.rs

@@ -1,17 +1,32 @@
 use rmcp::transport::streamable_http_client::StreamableHttpClientTransportConfig;
 use rmcp::transport::StreamableHttpClientTransport;
+use std::collections::HashMap;
 use std::sync::Arc;
 
-/// Build an HTTP (Streamable HTTP) transport from a URL.
+/// Build an HTTP (Streamable HTTP) transport from a URL with optional custom headers.
 /// Optionally attaches an Authorization bearer token.
+///
+/// NOTE: Custom headers are parsed but not yet applied due to rmcp v1.7.0 API limitations.
+/// The rmcp library's StreamableHttpClientTransportConfig does not expose a .header() method.
+/// Custom headers support is deferred until rmcp adds this capability or we find an alternative.
 pub fn build_http_transport(
     url: &str,
     auth_header: Option<&str>,
+    custom_headers: HashMap<String, String>,
 ) -> impl rmcp::transport::Transport<rmcp::RoleClient> {
+    // Log warning if custom headers are provided (not yet supported)
+    if !custom_headers.is_empty() {
+        tracing::warn!(
+            "Custom HTTP headers provided but not supported by rmcp v1.7.0: {:?}",
+            custom_headers.keys().collect::<Vec<_>>()
+        );
+    }
+
     let config = match auth_header {
         Some(token) => StreamableHttpClientTransportConfig::with_uri(Arc::from(url))
             .auth_header(token.to_string()),
         None => StreamableHttpClientTransportConfig::with_uri(Arc::from(url)),
     };
+
     StreamableHttpClientTransport::from_config(config)
 }

src-tauri/src/mcp/transport/stdio.rs

@@ -1,18 +1,134 @@
 use rmcp::transport::TokioChildProcess;
+use std::collections::HashMap;
 use std::path::Path;
 use tokio::process::Command;
 
-/// Build a stdio transport from a command path and argument list.
+/// Build a stdio transport from a command path, argument list, and environment variables.
 /// Rejects relative paths to prevent path traversal.
-pub fn build_stdio_transport(command: &str, args: &[String]) -> Result<TokioChildProcess, String> {
+/// Validates environment variable names to block known privilege escalation vectors.
+pub fn build_stdio_transport(
+    command: &str,
+    args: &[String],
+    env: HashMap<String, String>,
+) -> Result<TokioChildProcess, String> {
     if !Path::new(command).is_absolute() {
         return Err(format!(
             "stdio command must be an absolute path, got: {command}"
         ));
     }
 
+    // Validate env var names to block dangerous variables that could be used for privilege escalation
+    const DANGEROUS_ENV_VARS: &[&str] = &[
+        "LD_PRELOAD",
+        "LD_LIBRARY_PATH",
+        "DYLD_INSERT_LIBRARIES",
+        "DYLD_LIBRARY_PATH",
+        "DYLD_FRAMEWORK_PATH",
+        "DYLD_FALLBACK_LIBRARY_PATH",
+    ];
+
+    for key in env.keys() {
+        let upper_key = key.to_uppercase();
+        if DANGEROUS_ENV_VARS.contains(&upper_key.as_str()) {
+            return Err(format!(
+                "Dangerous environment variable '{key}' is not allowed for security reasons. \
+                 This variable could be used for privilege escalation attacks."
+            ));
+        }
+    }
+
     let mut cmd = Command::new(command);
     cmd.args(args);
 
+    // Apply environment variables
+    for (key, value) in env {
+        cmd.env(key, value);
+    }
+
     TokioChildProcess::new(cmd).map_err(|e| format!("Failed to spawn stdio process: {e}"))
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_rejects_relative_path() {
+        let result = build_stdio_transport("./mcp-server", &[], HashMap::new());
+        assert!(result.is_err());
+        if let Err(e) = result {
+            assert!(e.contains("absolute path"));
+        }
+    }
+
+    #[test]
+    fn test_rejects_dangerous_env_vars() {
+        let dangerous_vars = vec![
+            "LD_PRELOAD",
+            "LD_LIBRARY_PATH",
+            "DYLD_INSERT_LIBRARIES",
+            "DYLD_LIBRARY_PATH",
+            "DYLD_FRAMEWORK_PATH",
+            "DYLD_FALLBACK_LIBRARY_PATH",
+        ];
+
+        for var in dangerous_vars {
+            let mut env = HashMap::new();
+            env.insert(var.to_string(), "malicious.so".to_string());
+
+            let result = build_stdio_transport("/usr/bin/test", &[], env);
+            assert!(result.is_err(), "Should reject {}", var);
+            if let Err(err) = result {
+                assert!(
+                    err.contains("Dangerous environment variable"),
+                    "Error should mention dangerous variable: {}",
+                    err
+                );
+            }
+        }
+    }
+
+    #[test]
+    fn test_rejects_dangerous_env_vars_case_insensitive() {
+        let mut env = HashMap::new();
+        env.insert("ld_preload".to_string(), "malicious.so".to_string());
+
+        let result = build_stdio_transport("/usr/bin/test", &[], env);
+        assert!(result.is_err());
+        if let Err(err) = result {
+            assert!(err.contains("Dangerous environment variable"));
+        }
+    }
+
+    #[test]
+    fn test_allows_safe_env_vars() {
+        // Test that safe env vars pass validation (validation happens before spawn)
+        let safe_vars = vec![
+            ("DEBUG", "1"),
+            ("API_KEY", "secret123"),
+            ("PATH", "/usr/bin"),
+            ("HOME", "/home/user"),
+            ("GITHUB_PERSONAL_ACCESS_TOKEN", "ghp_token"),
+            ("LOG_LEVEL", "info"),
+        ];
+
+        for (key, value) in safe_vars {
+            let mut env = HashMap::new();
+            env.insert(key.to_string(), value.to_string());
+
+            // This will fail to spawn since /usr/bin/nonexistent doesn't exist,
+            // but if validation passed, error won't mention "Dangerous environment variable"
+            let result = build_stdio_transport("/usr/bin/nonexistent", &[], env);
+
+            // Validation passes (doesn't reject env var), spawn fails (command doesn't exist)
+            if let Err(err) = result {
+                assert!(
+                    !err.contains("Dangerous environment variable"),
+                    "Should not reject safe env var '{}', got: {}",
+                    key,
+                    err
+                );
+            }
+        }
+    }
+}

src/lib/INCIDENT_RESPONSE_FRAMEWORK.ts

@@ -0,0 +1,49 @@
+export const INCIDENT_RESPONSE_FRAMEWORK = `
+
+---
+
+## INCIDENT RESPONSE METHODOLOGY
+
+Follow this structured framework for every triage conversation. Each phase must be completed with evidence before advancing.
+
+### Phase 1: Detection & Evidence Gathering
+- **Do NOT propose fixes** until the problem is fully understood
+- Gather: error messages, timestamps, affected systems, scope of impact, recent changes
+- Ask: "What changed? When did it start? Who/what is affected? What has been tried?"
+- Record all evidence with UTC timestamps
+- Establish a clear problem statement before proceeding
+
+### Phase 2: Diagnosis & Hypothesis Testing
+- Apply the scientific method: form hypotheses, test them with evidence
+- **The 3-Fix Rule**: If you cannot confidently identify the root cause after 3 hypotheses, STOP and reassess your assumptions — you may be looking at the wrong system or the wrong layer
+- Check the most common causes first (Occam's Razor): DNS, certificates, disk space, permissions, recent deployments
+- Differentiate between symptoms and causes — treat causes, not symptoms
+- Use binary search to narrow scope: which component, which layer, which change
+
+### Phase 3: Root Cause Analysis with 5-Whys
+- Each "Why" must be backed by evidence, not speculation
+- If you cannot provide evidence for a "Why", state what investigation is needed to confirm
+- Look for systemic issues, not just proximate causes
+- The root cause should explain ALL observed symptoms, not just some
+- Common root cause categories: configuration drift, capacity exhaustion, dependency failure, race condition, human error in process
+
+### Phase 4: Resolution & Prevention
+- **Immediate fix**: What stops the bleeding right now? (rollback, restart, failover)
+- **Permanent fix**: What prevents recurrence? (code fix, config change, automation)
+- **Runbook update**: Document the fix for future oncall engineers
+- Verify the fix resolves ALL symptoms, not just the primary one
+- Monitor for regression after applying the fix
+
+### Phase 5: Post-Incident Review
+- Calculate incident metrics: MTTD (detect), MTTA (acknowledge), MTTR (resolve)
+- Conduct blameless post-mortem focused on systems and processes
+- Identify action items with owners and due dates
+- Categories: monitoring gaps, process improvements, technical debt, training needs
+- Ask: "What would have prevented this? What would have detected it faster? What would have resolved it faster?"
+
+### Communication Practices
+- State your current phase explicitly (e.g., "We are in Phase 2: Diagnosis")
+- Summarize findings at each phase transition
+- Flag assumptions clearly: "ASSUMPTION: ..." vs "CONFIRMED: ..."
+- When advancing the Why level, explicitly state the evidence chain
+`;

src/lib/tauriCommands.ts

@@ -562,6 +562,7 @@ export interface CreateMcpServerRequest {
   auth_type: "none" | "api_key" | "bearer" | "oauth2";
   auth_value?: string;
   enabled: boolean;
+  env_config?: string;
 }
 
 export interface UpdateMcpServerRequest {
@@ -572,6 +573,7 @@ export interface UpdateMcpServerRequest {
   auth_type?: "none" | "api_key" | "bearer" | "oauth2";
   auth_value?: string;
   enabled?: boolean;
+  env_config?: string;
 }
 
 // ─── MCP Commands ─────────────────────────────────────────────────────────────

src/pages/Settings/MCPServers.tsx

@@ -54,6 +54,42 @@ function parseTransportConfig(config: string): { command: string; args: string[]
   }
 }
 
+function parseEnvVars(input: string): Record<string, string> {
+  const result: Record<string, string> = {};
+  const pairs = input.trim().split(/\s+/).filter(Boolean);
+  for (const pair of pairs) {
+    const [key, ...valueParts] = pair.split("=");
+    if (key) {
+      result[key] = valueParts.join("=") || "";
+    }
+  }
+  return result;
+}
+
+function formatEnvVars(obj: Record<string, string>): string {
+  return Object.entries(obj)
+    .map(([k, v]) => `${k}=${v}`)
+    .join(" ");
+}
+
+function parseHeaders(input: string): Record<string, string> {
+  const result: Record<string, string> = {};
+  const pairs = input.trim().split(/\s+/).filter(Boolean);
+  for (const pair of pairs) {
+    const [key, ...valueParts] = pair.split(":");
+    if (key) {
+      result[key] = valueParts.join(":") || "";
+    }
+  }
+  return result;
+}
+
+function formatHeaders(obj: Record<string, string>): string {
+  return Object.entries(obj)
+    .map(([k, v]) => `${k}:${v}`)
+    .join(" ");
+}
+
 type StatusKey = McpServerStatus["status"];
 
 const statusColors: Record<StatusKey, string> = {
@@ -72,6 +108,9 @@ interface ServerForm {
   auth_type: "none" | "api_key" | "bearer" | "oauth2";
   auth_value: string;
   enabled: boolean;
+  plaintext_env: string;
+  encrypted_env: string;
+  http_headers: string;
 }
 
 const emptyForm: ServerForm = {
@@ -83,6 +122,9 @@ const emptyForm: ServerForm = {
   auth_type: "none",
   auth_value: "",
   enabled: true,
+  plaintext_env: "",
+  encrypted_env: "",
+  http_headers: "",
 };
 
 export default function MCPServers() {
@@ -155,6 +197,21 @@ export default function MCPServers() {
 
   const startEdit = (server: McpServer) => {
     const parsed = parseTransportConfig(server.transport_config);
+
+    // Parse plaintext env from transport_config.env
+    let plaintextEnv = "";
+    let httpHeaders = "";
+    try {
+      const config = JSON.parse(server.transport_config);
+      if (server.transport_type === "stdio" && config.env) {
+        plaintextEnv = formatEnvVars(config.env);
+      } else if (server.transport_type === "http" && config.headers) {
+        httpHeaders = formatHeaders(config.headers);
+      }
+    } catch {
+      // Invalid JSON, ignore
+    }
+
     setForm({
       name: server.name,
       url: server.url,
@@ -164,6 +221,9 @@ export default function MCPServers() {
       auth_type: server.auth_type,
       auth_value: "",
       enabled: server.enabled,
+      plaintext_env: plaintextEnv,
+      encrypted_env: "", // Never populate (security: don't show encrypted values)
+      http_headers: httpHeaders,
     });
     setEditServer(server);
     setIsAdding(true);
@@ -180,10 +240,25 @@ export default function MCPServers() {
     if (form.transport_type === "http" && !form.url) return;
     if (form.transport_type === "stdio" && !form.command) return;
 
+    // Build transport_config with env vars or headers
+    const plaintextEnvObj = parseEnvVars(form.plaintext_env);
+    const httpHeadersObj = parseHeaders(form.http_headers);
+
     const transportConfig =
       form.transport_type === "stdio"
-        ? JSON.stringify({ command: form.command, args: form.args.split(/\s+/).filter(Boolean) })
+        ? JSON.stringify({
-        : "{}";
+            command: form.command,
+            args: form.args.split(/\s+/).filter(Boolean),
+            env: plaintextEnvObj,
+          })
+        : JSON.stringify({
+            headers: httpHeadersObj,
+          });
+
+    // Build env_config (encrypted env) as JSON string
+    const encryptedEnvObj = parseEnvVars(form.encrypted_env);
+    const envConfig =
+      Object.keys(encryptedEnvObj).length > 0 ? JSON.stringify(encryptedEnvObj) : undefined;
 
     const url = form.transport_type === "http" ? form.url : "";
 
@@ -196,6 +271,7 @@ export default function MCPServers() {
           transport_config: transportConfig,
           auth_type: form.auth_type,
           enabled: form.enabled,
+          env_config: envConfig,
         };
         if (form.auth_value) {
           request.auth_value = form.auth_value;
@@ -210,6 +286,7 @@ export default function MCPServers() {
           auth_type: form.auth_type,
           auth_value: form.auth_value || undefined,
           enabled: form.enabled,
+          env_config: envConfig,
         };
         await createMcpServerCmd(request);
       }
@@ -475,6 +552,62 @@ export default function MCPServers() {
               </div>
             )}
 
+            {form.transport_type === "stdio" && (
+              <>
+                <Separator />
+                <div className="space-y-4">
+                  <div className="space-y-2">
+                    <Label>Environment Variables (Plaintext)</Label>
+                    <p className="text-xs text-muted-foreground">
+                      Space-separated KEY=value pairs for non-sensitive values (e.g., DEBUG=1 LOG_LEVEL=info)
+                    </p>
+                    <Input
+                      type="text"
+                      value={form.plaintext_env}
+                      onChange={(e) => setForm({ ...form, plaintext_env: e.target.value })}
+                      placeholder="KEY1=value1 KEY2=value2"
+                    />
+                  </div>
+
+                  <div className="space-y-2">
+                    <Label>Secure Environment Variables (Encrypted)</Label>
+                    <p className="text-xs text-muted-foreground">
+                      For sensitive values like API keys. Space-separated KEY=value pairs.
+                    </p>
+                    <Input
+                      type="password"
+                      value={form.encrypted_env}
+                      onChange={(e) => setForm({ ...form, encrypted_env: e.target.value })}
+                      placeholder={editServer ? "Leave blank to keep existing values" : "API_KEY=secret TOKEN=xyz"}
+                    />
+                    {editServer && (
+                      <p className="text-xs text-yellow-600 dark:text-yellow-400 mt-1">
+                        Encrypted values are stored securely and never displayed. Leave blank to preserve existing values.
+                      </p>
+                    )}
+                  </div>
+                </div>
+              </>
+            )}
+
+            {form.transport_type === "http" && (
+              <>
+                <Separator />
+                <div className="space-y-2">
+                  <Label>Custom Headers (Optional)</Label>
+                  <p className="text-xs text-muted-foreground">
+                    Space-separated KEY:value pairs for custom HTTP headers (e.g., X-API-Key:secret X-Custom:value)
+                  </p>
+                  <Input
+                    type="password"
+                    value={form.http_headers}
+                    onChange={(e) => setForm({ ...form, http_headers: e.target.value })}
+                    placeholder="X-API-Key:secret X-Custom-Header:value"
+                  />
+                </div>
+              </>
+            )}
+
             <Separator />
 
             <div className="flex items-center gap-2">