chore(cleanup): remove legacy aliases and cruft from codebase, docs, and tests

gemini-integration.lua

@@ -10,18 +10,6 @@ vim.api.nvim_create_autocmd({"VimEnter", "FocusGained", "BufEnter", "BufWritePos
         if #vim.api.nvim_list_uis() > 0 then
             local server_name = vim.v.servername
             if server_name then
-                -- 1. Legacy Disk Write (Fallback)
-                local home = os.getenv("HOME") or os.getenv("USERPROFILE")
-                if home then
-                    os.execute("mkdir -p " .. home .. "/.gemini")
-                    local path = home .. "/.gemini/active_nvim.txt"
-                    local f = io.open(path, "w")
-                    if f then
-                        f:write(server_name)
-                        f:close()
-                    end
-                end
-                
                 -- 2. V2 Telemetry Push (HTTP with Knowledge Projection + UDP Fast Mirror)
                 local file = vim.api.nvim_buf_get_name(0)
                 local cursor = vim.api.nvim_win_get_cursor(0)

instructions.md

@@ -59,7 +59,7 @@ The server registers 5 high-signal workflow prompts to initiate standardized age
 
 ## 5. Consolidated Smart Tools Architecture (11 Primary Tools)
 
-The server consolidates granular single-purpose tools into domain-named smart tools. Always prefer the consolidated tools over legacy aliases:
+The server consolidates granular single-purpose tools into domain-named smart tools.
 
 * **`tasks`**: Complete task lifecycle management.
   - `action: "add"`: Create a new task (requires `title`, optional `description`, `git_branch`, `repo_name`, `priority: "low" | "medium" | "high" | "urgent"`, `assigned_agent`, `verification_command`, `parent_id`, `dependencies`).

server/src/db.rs

@@ -117,75 +117,22 @@ pub fn init_redb(base: &Path) -> Arc<Database> {
         }
     };
 
-    // Ensure the table exists and migrate legacy JSON files
+    // Ensure the table exists
     match db.begin_write() {
         Ok(write_txn) => {
             let mut opened_ok = false;
-            if let Ok(mut table) = write_txn.open_table(STORE_TABLE) {
+            if let Ok(_) = write_txn.open_table(STORE_TABLE) {
                 opened_ok = true;
-                if !is_in_memory {
-                    let stores = vec![
-                        ("knowledge_graph_master", "knowledge_graph_master.json"),
-                        ("audit_ledger", "audit_ledger.json"),
-                        ("tasks", "tasks.json"),
-                        ("snippets", "snippets.json"),
-                        ("adrs", "adrs.json"),
-                        ("error_fixes", "error_fixes.json"),
-                        ("session_summaries", "session_summaries.json"),
-                        ("handoff_memos", "handoff_memos.json"),
-                        ("env_fingerprints", "env_fingerprints.json"),
-                        ("env_requirements", "env_requirements.json"),
-                        ("milestones", "milestones.json"),
-                        ("environments", "environments.json"),
-                        ("tech_debts", "tech_debts.json"),
-                        ("gates", "gates.json"),
-                        ("state_snapshots", "state_snapshots.json"),
-                        ("hypotheses", "hypotheses.json"),
-                        ("agent_signals", "agent_signals.json"),
-                    ];
-
-                    for (key, file_name) in stores.iter() {
-                        let is_missing = match table.get(*key) {
-                            Ok(res) => res.is_none(),
-                            Err(e) => {
-                                tracing::warn!("Failed to read key '{}' from redb: {}", key, e);
-                                false
-                            }
-                        };
-
-                        if is_missing {
-                            let json_path = base.join(file_name);
-                            if json_path.exists()
-                                && let Ok(data) = std::fs::read(&json_path)
-                                && serde_json::from_slice::<serde_json::Value>(&data).is_ok()
-                            {
-                                if let Err(e) = table.insert(*key, data.as_slice()) {
-                                    tracing::error!(
-                                        "Failed to insert migrated key '{}': {}",
-                                        key,
-                                        e
-                                    );
-                                } else {
-                                    let migrated_path = json_path.with_extension("json.migrated");
-                                    if std::fs::rename(&json_path, &migrated_path).is_err()
-                                        && migrated_path.exists()
-                                    {
-                                        let _ = std::fs::remove_file(&migrated_path);
-                                        let _ = std::fs::rename(&json_path, &migrated_path);
-                                    }
-                                }
-                            }
-                        }
-                    }
-                }
             }
-            if opened_ok && let Err(e) = write_txn.commit() {
+            if opened_ok {
-                tracing::error!("Failed to commit database migration transaction: {}", e);
+                if let Err(e) = write_txn.commit() {
+                    tracing::error!("Failed to commit database initialization transaction: {}", e);
+                }
             }
         }
         Err(e) => {
             tracing::error!(
-                "Failed to begin write transaction for redb migration: {}",
+                "Failed to begin write transaction for redb initialization: {}",
                 e
             );
         }

server/src/handlers/graph.rs

@@ -977,8 +977,8 @@ impl McpTool for GetSubgraphHandler {
 
     async fn execute(&self, args: Value, state: Arc<MemoryState>) -> crate::error::Result<String> {
         let req: GetSubgraphTool = serde_json::from_value(args).map_err(|e| e.to_string())?;
-        let root = req.root_entity.or(req.root_node).ok_or_else(|| {
+        let root = req.root_entity.ok_or_else(|| {
-            crate::error::AppError::Internal("root_entity or root_node is required".to_string())
+            crate::error::AppError::Internal("root_entity is required".to_string())
         })?;
         let depth = req.depth.unwrap_or(2);
         let format = req.format.unwrap_or(SubgraphFormat::Json);
@@ -1043,7 +1043,7 @@ impl McpTool for GetSubgraphHandler {
         }
 
         let result = serde_json::json!({
-            "root_node": root,
+            "root_entity": root,
             "depth": depth,
             "entities": matched_entities,
             "relations": matched_relations,

server/src/handlers/vision.rs

@@ -843,69 +843,7 @@ impl McpTool for ClipboardHandler {
                 })
                 .to_string())
             }
-            ClipboardAction::Read => {
-                let engine = ensure_ocr_engine().await;
 
-                let out = tokio::task::spawn_blocking(
-                    move || -> crate::error::Result<serde_json::Map<String, Value>> {
-                        let mut out = serde_json::Map::new();
-
-                        if let Some(text) = get_native_clipboard_text() {
-                            out.insert("text".into(), json!(text));
-                        }
-
-                        if let Some(dynamic_img) = get_native_clipboard_image() {
-                            let mut img = dynamic_img.clone();
-                            let max_dim = 1440;
-                            if img.width() > max_dim || img.height() > max_dim {
-                                img = img.resize(max_dim, max_dim, FilterType::Lanczos3);
-                            }
-                            let rgb_img = img.into_rgb8();
-
-                            let mut jpeg_bytes = std::io::Cursor::new(Vec::new());
-                            let mut encoder = image::codecs::jpeg::JpegEncoder::new_with_quality(
-                                &mut jpeg_bytes,
-                                88,
-                            );
-                            if encoder
-                                .encode(
-                                    &rgb_img,
-                                    rgb_img.width(),
-                                    rgb_img.height(),
-                                    image::ExtendedColorType::Rgb8,
-                                )
-                                .is_ok()
-                            {
-                                let bytes = jpeg_bytes.into_inner();
-
-                                let cache_dir = dirs::home_dir()
-                                    .unwrap_or_default()
-                                    .join(".gemini/mcp_memory/clipboard");
-                                let _ = std::fs::create_dir_all(&cache_dir);
-                                let file_path = cache_dir.join("clipboard_latest_image.jpg");
-                                if std::fs::write(&file_path, &bytes).is_ok() {
-                                    let path_str = file_path.to_string_lossy().to_string();
-                                    out.insert("image_path".into(), json!(path_str));
-                                    let wsl_path = to_wsl_path(&path_str);
-                                    out.insert("image_path_wsl".into(), json!(wsl_path));
-                                }
-                            }
-
-                            if let Some(eng) = engine
-                                && let Some(ocr_text) = perform_ocrs_ocr(eng, &dynamic_img)
-                            {
-                                out.insert("image_analysis".to_string(), json!(ocr_text.trim()));
-                            }
-                        }
-                        Ok(out)
-                    },
-                )
-                .await
-                .map_err(|e| crate::error::AppError::Internal(format!("Task panic: {}", e)))??;
-
-                state.record_activity("clipboard", "Read contents from OS clipboard", None);
-                Ok::<String, crate::error::AppError>(serde_yaml::to_string(&Value::Object(out))?)
-            }
             ClipboardAction::Write => {
                 let text_opt = req.text;
                 let image_path_opt = req.image_path;
@@ -1023,38 +961,7 @@ mod tests {
         );
     }
 
-    #[tokio::test]
-    async fn test_read_clipboard() {
-        let dir = tempdir().unwrap();
-        let state = Arc::new(MemoryState::new(dir.path().to_str().unwrap()));
-        let handler = ClipboardHandler;
 
-        let result = handler
-            .execute(json!({"action": "read"}), state)
-            .await
-            .map_err(|e| format!("Failed to read clipboard: {}", e))
-            .unwrap();
-
-        // Returns a JSON string, possibly {}
-        let parsed: serde_json::Value = serde_yaml::from_str(&result).unwrap();
-        assert!(parsed.is_object());
-    }
-
-    #[tokio::test]
-    async fn test_read_clipboard_empty() {
-        let dir = tempfile::tempdir().unwrap();
-        let state = Arc::new(MemoryState::new(dir.path().to_str().unwrap()));
-        let handler = ClipboardHandler;
-
-        let result = handler
-            .execute(serde_json::json!({"action": "read"}), state)
-            .await
-            .map_err(|e| format!("Failed to read clipboard: {}", e))
-            .unwrap();
-
-        let parsed: serde_json::Value = serde_yaml::from_str(&result).unwrap();
-        assert!(parsed.is_object());
-    }
 
     #[test]
     fn test_no_subprocess_clipboard_regression() {

server/src/instructions.md

@@ -59,7 +59,7 @@ The server registers 5 high-signal workflow prompts to initiate standardized age
 
 ## 5. Consolidated Smart Tools Architecture (11 Primary Tools)
 
-The server consolidates granular single-purpose tools into domain-named smart tools. Always prefer the consolidated tools over legacy aliases:
+The server consolidates granular single-purpose tools into domain-named smart tools.
 
 * **`tasks`**: Complete task lifecycle management.
   - `action: "add"`: Create a new task (requires `title`, optional `description`, `git_branch`, `repo_name`, `priority: "low" | "medium" | "high" | "urgent"`, `assigned_agent`, `verification_command`, `parent_id`, `dependencies`).

server/src/router.rs

@@ -1428,7 +1428,7 @@ mod tests {
             ("decisions", json!({"action": "query"})),
             ("tech_debt", json!({"action": "list"})),
             ("snippets", json!({"action": "search", "query": "test"})),
-            ("clipboard", json!({"action": "read"})),
+            ("clipboard", json!({"action": "history"})),
             ("environment", json!({"action": "read_fingerprint"})),
             ("omni_search", json!({"query": "test"})),
             ("get_project_health", json!({})),

server/src/tools.rs

@@ -172,8 +172,6 @@ pub enum SubgraphFormat {
 pub struct GetSubgraphTool {
     /// The root entity name to start the subgraph search from.
     pub root_entity: Option<String>,
-    /// Legacy alias for root_entity.
-    pub root_node: Option<String>,
     /// Maximum search depth (hops). Defaults to 2.
     pub depth: Option<u32>,
     /// Output format: 'json' (raw entities and relations) or 'markdown_tree' (compact topology tree). Defaults to 'json'.
@@ -1014,8 +1012,6 @@ pub enum ClipboardAction {
     History,
     #[serde(alias = "clear", alias = "CLEAR", alias = "Clear")]
     Clear,
-    #[serde(alias = "read", alias = "READ", alias = "Read")]
-    Read,
     #[serde(alias = "write", alias = "WRITE", alias = "Write")]
     Write,
 }
@@ -1026,7 +1022,6 @@ pub enum ClipboardAction {
 /// - 'text': Get latest clipboard text (or normalized Markdown if HTML was copied).
 /// - 'history': View recent clipboard history ring buffer (images and text with timestamps).
 /// - 'clear': Clear OS clipboard and memory cache.
-/// - 'read': Read current clipboard contents (legacy alias).
 /// - 'write': Write content to OS clipboard. Optional: text, html, files, image_path.
 ///
 /// Triggers: Call 'image' immediately when user says "look at image in clipboard", "see screenshot",