chore(server): remove dead scratch scripts, temporary files, and unused legacy modules

check_output.txt

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clippy_output.txt

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-warning: this can be `std::io::Error::other(_)`
-  --> stub\src\main.rs:76:72
-   |
-76 |             let stream = resp.bytes_stream().map(|res| res.map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e)));
-   |                                                                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-   |
-   = help: for further information visit https://rust-lang.github.io/rust-clippy/rust-1.98.0/index.html#io_other_error
-   = note: `#[warn(clippy::io_other_error)]` on by default
-help: use `std::io::Error::other`
-   |
-76 -             let stream = resp.bytes_stream().map(|res| res.map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e)));
-76 +             let stream = resp.bytes_stream().map(|res| res.map_err(|e| std::io::Error::other(e)));
-   |
-
-warning: stripping a prefix manually
-  --> stub\src\main.rs:93:40
-   |
-93 |                         println!("{}", &trimmed[6..]);
-   |                                        ^^^^^^^^^^^^^
-   |
-note: the prefix was tested here
-  --> stub\src\main.rs:91:24
-   |
-91 |                 } else if trimmed.starts_with("data: ") {
-   |                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-   = help: for further information visit https://rust-lang.github.io/rust-clippy/rust-1.98.0/index.html#manual_strip
-   = note: `#[warn(clippy::manual_strip)]` on by default
-help: try using the `strip_prefix` method
-   |
-91 ~                 } else if let Some(<stripped>) = trimmed.strip_prefix("data: ") {
-92 |                     if is_message {
-93 ~                         println!("{}", <stripped>);
-94 |                         is_message = false;
-95 |                     } else if is_endpoint {
-96 ~                         let ep = <stripped>;
-   |
-
-warning: redundant pattern matching
-   --> stub\src\main.rs:117:16
-    |
-117 |         if let Err(_) = std::net::TcpStream::connect(cli.target.replace("http://", "").replace("https://", "")) {
-    |                ^^^^^^
-    |
-    = help: for further information visit https://rust-lang.github.io/rust-clippy/rust-1.98.0/index.html#redundant_pattern_matching
-    = note: `#[warn(clippy::redundant_pattern_matching)]` on by default
-help: consider using `is_err()`
-    |
-117 -         if let Err(_) = std::net::TcpStream::connect(cli.target.replace("http://", "").replace("https://", "")) {
-117 +         if std::net::TcpStream::connect(cli.target.replace("http://", "").replace("https://", "")).is_err() {
-    |
-
-warning: `mcp-memory-stub` (bin "mcp-memory-stub") generated 3 warnings (run `cargo clippy --fix --bin "mcp-memory-stub" -p mcp-memory-stub -- ` to apply 2 suggestions)

dedup.py

@@ -1,14 +0,0 @@
-import re
-
-with open("server/src/handlers.rs", "r", encoding="utf-8") as f:
-    text = f.read()
-
-pattern = r'"(list_milestones|list_pinned_files|read_handoff_memos)" => \{\s*let req = parse_tool!\(args, id, ([a-zA-Z]+)\);\s*let mut [a-zA-Z_]+ = self\.state\.([a-zA-Z_]+)\.read\(\);\s*if let Some\(ns\) = req\.namespace \{\s*[a-zA-Z_]+\.retain\(\|.\| \w+\.namespace == ns\);\s*\}\s*let data = serde_json::to_string\(&[a-zA-Z_]+\)\.unwrap_or_default\(\);\s*Ok\(data\.to_string\(\)\)\s*\}'
-
-def repl(m):
-    return f'"{m.group(1)}" => handle_list_with_namespace!(self, {m.group(3)}, {m.group(2)}, args, id),'
-
-new_text = re.sub(pattern, repl, text)
-
-with open("server/src/handlers.rs", "w", encoding="utf-8") as f:
-    f.write(new_text)

dedup2.py

@@ -1,14 +0,0 @@
-import re
-
-with open("server/src/handlers.rs", "r", encoding="utf-8") as f:
-    text = f.read()
-
-pattern = r'"([a-zA-Z_]+)" => \{\s*(?:let req = parse_tool!\(args, id, ([a-zA-Z]+)\);\s*)?let data = serde_json::to_string\(&self\.state\.([a-zA-Z_]+)\.read\(\)\)\s*\.unwrap_or_else\(\|_\| "\[\]"\.to_string\(\)\);\s*Ok\(data\.to_string\(\)\)\s*\}'
-
-def repl(m):
-    return f'"{m.group(1)}" => {{\n    let data = serde_json::to_string(&self.state.{m.group(3)}.read()).unwrap_or_else(|_| "[]".to_string());\n    Ok(data)\n}},'
-
-new_text = re.sub(pattern, repl, text)
-
-with open("server/src/handlers.rs", "w", encoding="utf-8") as f:
-    f.write(new_text)

fix_warnings.py

@@ -1,40 +0,0 @@
-import re
-
-# 1. Fix stub/src/main.rs
-stub_path = r'C:\Users\reazul.ashraf\workspace\rust\mcp-memory\stub\src\main.rs'
-with open(stub_path, 'r', encoding='utf-8') as f:
-    content = f.read()
-content = content.replace('use tokio::io::AsyncBufReadExt;\n', '')
-with open(stub_path, 'w', encoding='utf-8') as f:
-    f.write(content)
-
-# 2. Fix nvim-core/src/lib.rs
-nvim_path = r'C:\Users\reazul.ashraf\workspace\rust\mcp-memory\nvim-core\src\lib.rs'
-with open(nvim_path, 'r', encoding='utf-8') as f:
-    content = f.read()
-content = content.replace(
-    'use tokio::io::{AsyncBufReadExt, AsyncReadExt, AsyncWriteExt, BufReader};',
-    'use tokio::io::{AsyncReadExt, AsyncWriteExt};'
-)
-with open(nvim_path, 'w', encoding='utf-8') as f:
-    f.write(content)
-
-# 3. Fix server/src/store.rs
-store_path = r'C:\Users\reazul.ashraf\workspace\rust\mcp-memory\server\src\store.rs'
-with open(store_path, 'r', encoding='utf-8') as f:
-    content = f.read()
-
-inspect_method = """    pub fn inspect<F, R>(&self, f: F) -> R
-    where
-        F: FnOnce(&T) -> R,
-    {
-        let lock = self.cache.read().unwrap();
-        f(&lock)
-    }
-
-"""
-content = content.replace(inspect_method, "")
-with open(store_path, 'w', encoding='utf-8') as f:
-    f.write(content)
-
-print("Warnings fixed!")

patch_nvim.py

@@ -1,168 +0,0 @@
-import re
-import sys
-
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\nvim-core\\src\\lib.rs', 'r', encoding='utf-8') as f:
-    content = f.read()
-
-start_pattern = r'#\[cfg\(windows\)\]\nasync fn call_nvim'
-end_pattern = r'async fn send_nvim_command'
-
-start_idx = re.search(start_pattern, content).start()
-end_idx = re.search(end_pattern, content).start()
-
-new_code = """use std::sync::LazyLock;
-use std::sync::Arc;
-use tokio::sync::{Mutex, mpsc, oneshot};
-use std::collections::HashMap;
-use tokio::io::{AsyncReadExt, AsyncWriteExt};
-
-pub struct NvimRequest {
-    pub msgid_str: String,
-    pub req: rmpv::Value,
-    pub reply: oneshot::Sender<Result<rmpv::Value, String>>,
-}
-
-static NVIM_CONN: LazyLock<Arc<Mutex<Option<mpsc::Sender<NvimRequest>>>>> = LazyLock::new(|| Arc::new(Mutex::new(None)));
-
-async fn get_nvim_connection() -> Result<mpsc::Sender<NvimRequest>, String> {
-    let mut conn_lock = NVIM_CONN.lock().await;
-    if let Some(sender) = conn_lock.as_ref() {
-        if !sender.is_closed() {
-            return Ok(sender.clone());
-        }
-    }
-
-    tracing::info!("Establishing new persistent connection to Neovim");
-    let socket_path = get_socket_path().await?;
-
-    #[cfg(windows)]
-    let stream = {
-        use tokio::net::windows::named_pipe::ClientOptions;
-        ClientOptions::new().open(&socket_path).map_err(|e| e.to_string())?
-    };
-
-    #[cfg(unix)]
-    let stream = {
-        use tokio::net::UnixStream;
-        UnixStream::connect(socket_path).await.map_err(|e| e.to_string())?
-    };
-
-    let (mut read_half, mut write_half) = tokio::io::split(stream);
-    let (tx, mut rx) = mpsc::channel::<NvimRequest>(32);
-    let pending_requests: Arc<Mutex<HashMap<String, oneshot::Sender<Result<rmpv::Value, String>>>>> = Arc::new(Mutex::new(HashMap::new()));
-
-    // Write task
-    let pending_clone = Arc::clone(&pending_requests);
-    tokio::spawn(async move {
-        while let Some(req) = rx.recv().await {
-            let mut buf = Vec::new();
-            if let Err(e) = rmpv::encode::write_value(&mut buf, &req.req) {
-                let _ = req.reply.send(Err(e.to_string()));
-                continue;
-            }
-            
-            pending_clone.lock().await.insert(req.msgid_str.clone(), req.reply);
-            
-            if write_half.write_all(&buf).await.is_err() {
-                tracing::error!("Failed to write to Neovim socket");
-                break;
-            }
-        }
-    });
-
-    // Read task
-    let pending_clone2 = Arc::clone(&pending_requests);
-    tokio::spawn(async move {
-        let mut resp_buf = Vec::new();
-        let mut chunk = vec![0u8; 8192];
-        let mut offset = 0;
-
-        loop {
-            let mut cursor = std::io::Cursor::new(&resp_buf[offset..]);
-            match rmpv::decode::read_value(&mut cursor) {
-                Ok(val) => {
-                    offset += cursor.position() as usize;
-
-                    if let rmpv::Value::Array(ref arr) = val {
-                        if arr.len() >= 4 && arr[0] == rmpv::Value::Integer(1.into()) {
-                            let msgid = &arr[1];
-                            let msgid_str = format!("{:?}", msgid);
-                            
-                            if let Some(reply_sender) = pending_clone2.lock().await.remove(&msgid_str) {
-                                let _ = reply_sender.send(Ok(val));
-                            }
-                        }
-                    }
-                    // Trim buffer if it gets too large
-                    if offset > 1024 * 1024 {
-                        resp_buf.drain(..offset);
-                        offset = 0;
-                    }
-                    continue;
-                }
-                Err(_) => {
-                    if offset > 0 {
-                        resp_buf.drain(..offset);
-                        offset = 0;
-                    }
-                    
-                    let read_future = read_half.read(&mut chunk);
-                    match tokio::time::timeout(tokio::time::Duration::from_secs(60), read_future).await {
-                        Ok(Ok(n)) if n > 0 => {
-                            resp_buf.extend_from_slice(&chunk[..n]);
-                        }
-                        _ => {
-                            tracing::error!("Neovim socket read loop closed or timeout");
-                            break;
-                        }
-                    }
-                }
-            }
-        }
-        
-        // Cleanup pending requests on disconnect
-        let mut pending = pending_clone2.lock().await;
-        for (_, sender) in pending.drain() {
-            let _ = sender.send(Err("Connection closed".to_string()));
-        }
-    });
-
-    *conn_lock = Some(tx.clone());
-    Ok(tx)
-}
-
-async fn call_nvim(req: rmpv::Value) -> Result<rmpv::Value, String> {
-    let msgid = if let rmpv::Value::Array(ref arr) = req {
-        if arr.len() > 1 {
-            arr[1].clone()
-        } else {
-            rmpv::Value::Nil
-        }
-    } else {
-        rmpv::Value::Nil
-    };
-    
-    let msgid_str = format!("{:?}", msgid);
-    let tx = get_nvim_connection().await?;
-    let (reply_tx, reply_rx) = oneshot::channel();
-    
-    tx.send(NvimRequest {
-        msgid_str,
-        req,
-        reply: reply_tx,
-    }).await.map_err(|_| "Failed to send request to Neovim connection manager")?;
-    
-    match tokio::time::timeout(tokio::time::Duration::from_secs(10), reply_rx).await {
-        Ok(Ok(res)) => res,
-        Ok(Err(_)) => Err("Response channel dropped".to_string()),
-        Err(_) => Err("Timeout waiting for Neovim response".to_string()),
-    }
-}
-
-"""
-
-new_content = content[:start_idx] + new_code + content[end_idx:]
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\nvim-core\\src\\lib.rs', 'w', encoding='utf-8') as f:
-    f.write(new_content)
-
-print("Patched!")

patch_nvim_macro.py

@@ -1,40 +0,0 @@
-import re
-import sys
-
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\nvim-core\\src\\lib.rs', 'r', encoding='utf-8') as f:
-    content = f.read()
-
-macro_def = """
-macro_rules! send_text_result {
-    ($id:expr, $text:expr) => {
-        send_response(JsonRpcResponse {
-            jsonrpc: "2.0".to_string(),
-            id: $id,
-            result: Some(json!({
-                "content": [{"type": "text", "text": $text}]
-            })),
-            error: None,
-        }).await;
-    };
-}
-"""
-
-if "macro_rules! send_text_result" not in content:
-    idx = content.find("pub async fn run_mcp_loop")
-    content = content[:idx] + macro_def + "\n" + content[idx:]
-
-# Find tools/call block
-tools_call_idx = content.find('"tools/call" => {')
-if tools_call_idx != -1:
-    block = content[tools_call_idx:]
-    
-    # Replace the verbose blocks
-    pattern = r'send_response\(JsonRpcResponse \{\s*jsonrpc: "2\.0"\.to_string\(\),\s*id,\s*result: Some\(json!\(\{\s*"content": \[\{"type": "text", "text": (.*?)\}\]\s*\}\)\),\s*error: None,\s*\}\)\s*\.await;'
-    
-    new_block = re.sub(pattern, r'send_text_result!(id.clone(), \1);', block)
-    
-    content = content[:tools_call_idx] + new_block
-
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\nvim-core\\src\\lib.rs', 'w', encoding='utf-8') as f:
-    f.write(content)
-print("Patched nvim macro")

patch_stub.py

@@ -1,15 +0,0 @@
-import re
-import sys
-
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\stub\\src\\main.rs', 'r', encoding='utf-8') as f:
-    content = f.read()
-
-start1 = r'let mut log_prefix = String::from\("Message"\);\n\s*if let Ok\(v\) = serde_json::from_str::<serde_json::Value>\(&msg\) \{[\s\S]*?log_prefix = format!\("Response id=\{\}", res_id\);\n\s*\}\n\s*\}'
-content = re.sub(start1, r'let log_prefix = logger::extract_log_prefix(&msg, false);', content)
-
-start2 = r'let mut log_prefix = String::from\("Message"\);\n\s*if let Ok\(v\) = serde_json::from_str::<serde_json::Value>\(&text\) \{[\s\S]*?log_prefix = format!\("Response id=\{\} \[Error: \{\}\]", id, is_error\);\n\s*\}'
-content = re.sub(start2, r'let log_prefix = logger::extract_log_prefix(&text, true);', content)
-
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\stub\\src\\main.rs', 'w', encoding='utf-8') as f:
-    f.write(content)
-print("Patched stub")

patch_tests.py

@@ -1,12 +0,0 @@
-import re
-
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\nvim-core\\src\\lib.rs', 'r', encoding='utf-8') as f:
-    content = f.read()
-
-content = content.replace('read_message(&mut reader)', 'mcp_stdio::read_mcp_message(&mut reader)')
-content = content.replace('let req = mcp_stdio::read_mcp_message(&mut reader).await.unwrap();', 'let raw = mcp_stdio::read_mcp_message(&mut reader).await.unwrap();\n        let req: JsonRpcRequest = serde_json::from_str(&raw).unwrap();')
-content = content.replace('let req = mcp_stdio::read_mcp_message(&mut reader).await;', 'let req = mcp_stdio::read_mcp_message(&mut reader).await;')
-
-with open('C:\\Users\\reazul.ashraf\\workspace\\rust\\mcp-memory\\nvim-core\\src\\lib.rs', 'w', encoding='utf-8') as f:
-    f.write(content)
-print("Patched tests")

server/fix_descriptions.py

@@ -1,24 +0,0 @@
-import re
-
-with open(r'C:\Users\reazul.ashraf\workspace\rust\mcp-memory\server\src\handlers.rs', 'r', encoding='utf-8') as f:
-    content = f.read()
-
-content = content.replace(
-    'crate::mcp::tool_def::<GenerateStandupReportTool>(\n                        "generate_standup_report",\n                        "",\n                    )',
-    'crate::mcp::tool_def::<GenerateStandupReportTool>(\n                        "generate_standup_report",\n                        "Generate a standup report summarizing recent work, blockers, and next steps.",\n                    )'
-)
-
-content = content.replace(
-    'crate::mcp::tool_def::<GetEnvironmentDetailsTool>(\n                        "get_environment_details",\n                        "",\n                    )',
-    'crate::mcp::tool_def::<GetEnvironmentDetailsTool>(\n                        "get_environment_details",\n                        "Get detailed information about a specific deployment environment.",\n                    )'
-)
-
-content = content.replace(
-    'crate::mcp::tool_def::<ListContextWorkspacesTool>(\n                        "list_context_workspaces",\n                        "",\n                    )',
-    'crate::mcp::tool_def::<ListContextWorkspacesTool>(\n                        "list_context_workspaces",\n                        "List all saved context workspaces.",\n                    )'
-)
-
-with open(r'C:\Users\reazul.ashraf\workspace\rust\mcp-memory\server\src\handlers.rs', 'w', encoding='utf-8') as f:
-    f.write(content)
-
-print("Descriptions fixed.")

server/src/bake_nvim_safeguards.py

@@ -1,62 +0,0 @@
-import os
-import re
-
-def bake_nvim_safeguards():
-    filepath = 'nvim-core/src/lib.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    # 1. We're going to inject an AST-level safeguard inside "nvim_execute_lua"
-    # Find the execute_lua block
-    target = """                        "nvim_execute_lua" => {
-                            if let Some(code) = args.get("code").and_then(|v| v.as_str()) {
-                                match execute_nvim_lua(code).await {"""
-    
-    safeguarded = """                        "nvim_execute_lua" => {
-                            if let Some(code) = args.get("code").and_then(|v| v.as_str()) {
-                                // BAKE IN: Block interactive prompts that cause server deadlocks
-                                let lower_code = code.to_lowercase();
-                                if lower_code.contains("vim.fn.input") || lower_code.contains("vim.ui.select") || lower_code.contains("vim.fn.confirm") || lower_code.contains("vim.ui.input") {
-                                    send_error(id, -32600, "CRITICAL ERROR: Interactive Lua functions (input, select, confirm) are strictly forbidden via MCP as they will hang the headless server.").await;
-                                    return;
-                                }
-                                // Block the 'c' confirm flag in vim.cmd substitutions
-                                if (code.contains("vim.cmd") || code.contains("vim.api.nvim_command")) && code.contains("%s") && code.contains("c") {
-                                    // A rough heuristic to block `%s/foo/bar/gc`
-                                    if regex::Regex::new(r"%s.*/.*c").unwrap().is_match(code) {
-                                        send_error(id, -32600, "CRITICAL ERROR: The 'c' (confirm) flag in Neovim substitutions is strictly forbidden via MCP as it triggers an interactive prompt that hangs the headless server. Use '/ge' instead.").await;
-                                        return;
-                                    }
-                                }
-
-                                match execute_nvim_lua(code).await {"""
-    
-    if target in content:
-        # Also need to add regex as a dependency or just use basic string matching.
-        # Let's just use basic string matching for the %s block to avoid adding the regex crate to nvim-core if not present
-        
-        safeguarded_no_regex = """                        "nvim_execute_lua" => {
-                            if let Some(code) = args.get("code").and_then(|v| v.as_str()) {
-                                // BAKE IN: Block interactive prompts that cause server deadlocks
-                                let lower_code = code.to_lowercase();
-                                if lower_code.contains("vim.fn.input") || lower_code.contains("vim.ui.select") || lower_code.contains("vim.fn.confirm") || lower_code.contains("vim.ui.input") {
-                                    send_error(id, -32600, "CRITICAL ERROR: Interactive Lua functions (input, select, confirm) are strictly forbidden via MCP as they will hang the headless server.").await;
-                                    return;
-                                }
-                                // Block the 'c' confirm flag in vim.cmd substitutions
-                                if (code.contains("vim.cmd") || code.contains("vim.api.nvim_command")) && code.contains("%s") && (code.contains("gc'") || code.contains('gc"') || code.contains("gc\\n") || code.contains("c'") || code.contains('c"')) {
-                                     send_error(id, -32600, "CRITICAL ERROR: The 'c' (confirm) flag in Neovim substitutions is strictly forbidden via MCP as it triggers an interactive prompt that hangs the headless server. Use '/g' or '/ge' instead.").await;
-                                     return;
-                                }
-
-                                match execute_nvim_lua(code).await {"""
-        
-        content = content.replace(target, safeguarded_no_regex)
-        print("Baked safeguards into nvim_execute_lua")
-        
-        with open(filepath, 'w', encoding='utf-8') as f:
-            f.write(content)
-    else:
-        print("Could not find nvim_execute_lua block")
-
-bake_nvim_safeguards()

server/src/bin_replace2.py

@@ -1,150 +0,0 @@
-import os
-
-def rewrite_graph():
-    with open('server/src/handlers_v2/graph.rs', 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    old_block = """        let mut included: HashSet<&str> = HashSet::new();
-        let mut to_draw = Vec::new();
-
-        state.read_graph(|full| {
-            for (name, e) in &full.entities {
-                if let Some(ns) = &req.namespace
-                    && e.namespace != *ns
-                {
-                    continue;
-                }
-                if query.is_empty()
-                    || contains_ignore_ascii_case(name, &query)
-                    || contains_ignore_ascii_case(&e.entity_type, &query)
-                {
-                    included.insert(name.as_str());
-                }
-            }
-
-            for r in &full.relations {
-                if let Some(ns) = &req.namespace
-                    && r.namespace != *ns
-                {
-                    continue;
-                }
-                if query.is_empty() || included.contains(r.from.as_str()) || included.contains(r.to.as_str()) {
-                    included.insert(r.from.as_str());
-                    included.insert(r.to.as_str());
-                    to_draw.push(r.clone());
-                }
-            }
-        });
-        use std::fmt::Write;
-        let mut output = String::with_capacity(included.len() * 40 + to_draw.len() * 60);
-        output.push_str("graph TD;\\n");
-
-        let sanitize = |s: &str, id_mode: bool| -> String {
-            let mut out = String::with_capacity(s.len());
-            for c in s.chars() {
-                if c != '"' && c != '(' && c != ')' {
-                    if id_mode && (c == ' ' || c == '-' || c == '.') {
-                        out.push('_');
-                    } else {
-                        out.push(c);
-                    }
-                }
-            }
-            out
-        };
-
-        for name in &included {
-            let _ = writeln!(
-                output,
-                "    id_{}[\\"{}\\"];",
-                sanitize(name, true),
-                sanitize(name, false)
-            );
-        }
-        for r in to_draw {
-            let _ = writeln!(
-                output,
-                "    id_{}-->|\\"{}\\"|id_{};",
-                sanitize(&r.from, true),
-                r.relation_type.replace("\\"", ""),
-                sanitize(&r.to, true)
-            );
-        }"""
-
-    new_block = """        use std::fmt::Write;
-        let mut output = state.read_graph(|full| {
-            let mut included: HashSet<&str> = HashSet::new();
-            let mut to_draw = Vec::new();
-
-            for (name, e) in &full.entities {
-                if let Some(ns) = &req.namespace
-                    && e.namespace != *ns
-                {
-                    continue;
-                }
-                if query.is_empty()
-                    || contains_ignore_ascii_case(name, &query)
-                    || contains_ignore_ascii_case(&e.entity_type, &query)
-                {
-                    included.insert(name.as_str());
-                }
-            }
-
-            for r in &full.relations {
-                if let Some(ns) = &req.namespace
-                    && r.namespace != *ns
-                {
-                    continue;
-                }
-                if query.is_empty() || included.contains(r.from.as_str()) || included.contains(r.to.as_str()) {
-                    included.insert(r.from.as_str());
-                    included.insert(r.to.as_str());
-                    to_draw.push(r.clone());
-                }
-            }
-
-            let mut out = String::with_capacity(included.len() * 40 + to_draw.len() * 60);
-            out.push_str("graph TD;\\n");
-
-            let sanitize = |s: &str, id_mode: bool| -> String {
-                let mut o = String::with_capacity(s.len());
-                for c in s.chars() {
-                    if c != '"' && c != '(' && c != ')' {
-                        if id_mode && (c == ' ' || c == '-' || c == '.') {
-                            o.push('_');
-                        } else {
-                            o.push(c);
-                        }
-                    }
-                }
-                o
-            };
-
-            for name in &included {
-                let _ = writeln!(
-                    out,
-                    "    id_{}[\\"{}\\"];",
-                    sanitize(name, true),
-                    sanitize(name, false)
-                );
-            }
-            for r in to_draw {
-                let _ = writeln!(
-                    out,
-                    "    id_{}-->|\\"{}\\"|id_{};",
-                    sanitize(&r.from, true),
-                    r.relation_type.replace("\\"", ""),
-                    sanitize(&r.to, true)
-                );
-            }
-            out
-        });"""
-
-    if old_block in content:
-        with open('server/src/handlers_v2/graph.rs', 'w', encoding='utf-8') as f:
-            f.write(content.replace(old_block, new_block))
-        print("Replaced visualize_graph")
-    else:
-        print("Could not find old block")
-
-rewrite_graph()

server/src/bin_test.rs

@@ -1,10 +0,0 @@
-use rmcp::model::{InitializeResult, ServerCapabilities};
-
-fn main() {
-    let init = InitializeResult::new(ServerCapabilities::builder().enable_tools().build())
-        .with_server_info(rmcp::model::Implementation::new(
-            "gemini-mcp-memory",
-            "3.0.0",
-        ));
-    println!("{}", serde_json::to_string_pretty(&init).unwrap());
-}

server/src/fix_env_ws.py

@@ -1,61 +0,0 @@
-import os
-
-def fix_env_and_workspaces():
-    filepath = 'server/src/handlers_v2/env.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    old_env = """        let fps = state.env_fingerprints.read();
-        if let Some(fp) = fps.get(&req.namespace) {"""
-
-    new_env = """        let data = state.env_fingerprints.read_with(|fps| {
-            fps.get(&req.namespace).cloned()
-        });
-        if let Some(fp) = data {"""
-
-    if old_env in content:
-        content = content.replace(old_env, new_env)
-        print('Replaced env read')
-    else:
-        print('Could not find old_env')
-    
-    with open(filepath, 'w', encoding='utf-8') as f:
-        f.write(content)
-
-    filepath = 'server/src/handlers_v2/workspaces.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    old_ws = """        let query = req.query.to_lowercase();
-        let snippets = state.snippets.read();
-        let mut results = Vec::new();
-        for s in snippets {
-            if contains_ignore_ascii_case(&s.name, &query)
-                || contains_ignore_ascii_case(&s.description, &query)
-                || contains_ignore_ascii_case(&s.language, &query)
-            {
-                results.push(s);
-            }
-        }
-        let data = serde_json::to_string(&results).unwrap_or_default();"""
-
-    new_ws = """        let query = req.query.to_lowercase();
-        let data = state.snippets.read_with(|snippets| {
-            let results: Vec<_> = snippets.iter().filter(|s| {
-                contains_ignore_ascii_case(&s.name, &query)
-                    || contains_ignore_ascii_case(&s.description, &query)
-                    || contains_ignore_ascii_case(&s.language, &query)
-            }).cloned().collect();
-            serde_json::to_string(&results).unwrap_or_default()
-        });"""
-
-    if old_ws in content:
-        content = content.replace(old_ws, new_ws)
-        print('Replaced workspaces read')
-    else:
-        print('Could not find old_ws')
-
-    with open(filepath, 'w', encoding='utf-8') as f:
-        f.write(content)
-
-fix_env_and_workspaces()

server/src/fix_main.py

@@ -1,60 +0,0 @@
-import os
-
-def fix_main_stats():
-    filepath = 'server/src/main.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    old_stats = """                        let (entities, relations) = {
-                            let graph = state_clone.get_full_graph();
-                            (graph.entities.len(), graph.relations.len())
-                        };
-                        let tasks = state_clone.tasks.read().len();
-                        let snippets = state_clone.snippets.read().len();
-                        let tech_debts = state_clone.tech_debts.read().len();
-                        let adrs = state_clone.adrs.read().len();
-
-                        let ledger = state_clone.ledger.read().len();
-                        let sticky = state_clone.sticky.read().len();
-                        let error_fixes = state_clone.error_fixes.read().len();
-                        let pinned_files = state_clone.pinned_files.read().len();
-                        let session_summaries = state_clone.session_summaries.read().len();
-                        let handoff_memos = state_clone.handoff_memos.read().len();
-                        let env_fingerprints = state_clone.env_fingerprints.read().len();
-                        let env_requirements = state_clone.env_requirements.read().len();
-                        let milestones = state_clone.milestones.read().len();
-                        let environments = state_clone.environments.read().len();
-                        let pr_checklists = state_clone.pr_checklists.read().len();
-                        let gates = state_clone.gates.read().len();
-                        let context_workspaces = state_clone.context_workspaces.read().len();"""
-
-    new_stats = """                        let (entities, relations) = state_clone.read_graph(|g| (g.entities.len(), g.relations.len()));
-                        let tasks = state_clone.tasks.read_with(|items| items.len());
-                        let snippets = state_clone.snippets.read_with(|items| items.len());
-                        let tech_debts = state_clone.tech_debts.read_with(|items| items.len());
-                        let adrs = state_clone.adrs.read_with(|items| items.len());
-
-                        let ledger = state_clone.ledger.read_with(|items| items.len());
-                        let sticky = state_clone.sticky.read_with(|items| items.len());
-                        let error_fixes = state_clone.error_fixes.read_with(|items| items.len());
-                        let pinned_files = state_clone.pinned_files.read_with(|items| items.len());
-                        let session_summaries = state_clone.session_summaries.read_with(|items| items.len());
-                        let handoff_memos = state_clone.handoff_memos.read_with(|items| items.len());
-                        let env_fingerprints = state_clone.env_fingerprints.read_with(|items| items.len());
-                        let env_requirements = state_clone.env_requirements.read_with(|items| items.len());
-                        let milestones = state_clone.milestones.read_with(|items| items.len());
-                        let environments = state_clone.environments.read_with(|items| items.len());
-                        let pr_checklists = state_clone.pr_checklists.read_with(|items| items.len());
-                        let gates = state_clone.gates.read_with(|items| items.len());
-                        let context_workspaces = state_clone.context_workspaces.read_with(|items| items.len());"""
-
-    if old_stats in content:
-        content = content.replace(old_stats, new_stats)
-        print('Replaced stats reads')
-    else:
-        print('Could not find old_stats')
-
-    with open(filepath, 'w', encoding='utf-8') as f:
-        f.write(content)
-
-fix_main_stats()

server/src/fix_meta.py

@@ -1,111 +0,0 @@
-import os
-
-def fix_meta():
-    filepath = 'server/src/handlers_v2/meta.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    old_omni = """        let q = req.query.to_lowercase();
-        let tech_debts: Vec<_> = state
-            .tech_debts
-            .read()
-            .into_iter()
-            .filter(|d| {
-                req.namespace.as_ref().is_none_or(|ns| d.namespace == *ns)
-                    && (contains_ignore_ascii_case(&d.description, &q)
-                        || contains_ignore_ascii_case(&d.ideal_solution, &q))
-            })
-            .collect();
-        let memos: Vec<_> = state
-            .handoff_memos
-            .read()
-            .into_iter()
-            .filter(|m| {
-                req.namespace.as_ref().is_none_or(|ns| m.namespace == *ns)
-                    && contains_ignore_ascii_case(&m.content, &q)
-            })
-            .collect();
-        let error_fixes: Vec<_> = state
-            .error_fixes
-            .read()
-            .into_iter()
-            .filter(|f| {
-                contains_ignore_ascii_case(&f.signature, &q)
-                    || contains_ignore_ascii_case(&f.solution, &q)
-            })
-            .collect();"""
-
-    new_omni = """        let q = req.query.to_lowercase();
-        let tech_debts = state.tech_debts.read_with(|debts| {
-            debts.iter().filter(|d| {
-                req.namespace.as_ref().is_none_or(|ns| d.namespace == *ns)
-                    && (contains_ignore_ascii_case(&d.description, &q)
-                        || contains_ignore_ascii_case(&d.ideal_solution, &q))
-            }).cloned().collect::<Vec<_>>()
-        });
-        let memos = state.handoff_memos.read_with(|memos| {
-            memos.iter().filter(|m| {
-                req.namespace.as_ref().is_none_or(|ns| m.namespace == *ns)
-                    && contains_ignore_ascii_case(&m.content, &q)
-            }).cloned().collect::<Vec<_>>()
-        });
-        let error_fixes = state.error_fixes.read_with(|fixes| {
-            fixes.iter().filter(|f| {
-                contains_ignore_ascii_case(&f.signature, &q)
-                    || contains_ignore_ascii_case(&f.solution, &q)
-            }).cloned().collect::<Vec<_>>()
-        });"""
-
-    if old_omni in content:
-        content = content.replace(old_omni, new_omni)
-        print('Replaced omni_search vecs')
-    else:
-        print('Could not find old_omni')
-
-    old_health = """        let active_tasks = state
-            .tasks
-            .read()
-            .into_iter()
-            .filter(|t| t.status != "done")
-            .count();
-        let unresolved_debt = state
-            .tech_debts
-            .read()
-            .into_iter()
-            .filter(|d| d.namespace == req.namespace && !d.is_resolved)
-            .count();
-        let unread_memos = state
-            .handoff_memos
-            .read()
-            .into_iter()
-            .filter(|m| m.namespace == req.namespace)
-            .count();
-        let active_milestones = state
-            .milestones
-            .read()
-            .into_iter()
-            .filter(|m| m.namespace == req.namespace && m.status != "done")
-            .count();
-        let remaining_checklists = state
-            .pr_checklists
-            .read()
-            .into_iter()
-            .filter(|c| c.namespace == req.namespace)
-            .count();"""
-
-    new_health = """        let active_tasks = state.tasks.read_with(|tasks| tasks.iter().filter(|t| t.status != "done").count());
-        let unresolved_debt = state.tech_debts.read_with(|debts| debts.iter().filter(|d| d.namespace == req.namespace && !d.is_resolved).count());
-        let unread_memos = state.handoff_memos.read_with(|memos| memos.iter().filter(|m| m.namespace == req.namespace).count());
-        let active_milestones = state.milestones.read_with(|milestones| milestones.iter().filter(|m| m.namespace == req.namespace && m.status != "done").count());
-        let remaining_checklists = state.pr_checklists.read_with(|checklists| checklists.iter().filter(|c| c.namespace == req.namespace).count());"""
-
-    if old_health in content:
-        content = content.replace(old_health, new_health)
-        print('Replaced health counters')
-    else:
-        print('Could not find old_health')
-
-    with open(filepath, 'w', encoding='utf-8') as f:
-        f.write(content)
-
-fix_meta()

server/src/fix_msgid.py

@@ -1,44 +0,0 @@
-import os
-import re
-
-def fix_nvim_msgid():
-    filepath = 'nvim-core/src/lib.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    # Add atomic import and static var if not exists
-    if 'static NEXT_MSGID' not in content:
-        atomic_def = "use std::sync::atomic::{AtomicU64, Ordering};\nstatic NEXT_MSGID: AtomicU64 = AtomicU64::new(1);\n"
-        # Find NVIM_CONN
-        conn_idx = content.find('static NVIM_CONN')
-        if conn_idx != -1:
-            content = content[:conn_idx] + atomic_def + content[conn_idx:]
-
-    # Replace all hardcoded msgid
-    # e.g., RmpValue::Integer(1.into()), // msgid
-    # with: let msgid = NEXT_MSGID.fetch_add(1, Ordering::SeqCst); ... RmpValue::Integer(msgid.into()),
-
-    # We need to insert `let msgid = NEXT_MSGID.fetch_add(1, Ordering::SeqCst);` before `let req = RmpValue::Array(vec![`
-    
-    # We will use regex to find the blocks
-    funcs = [
-        ('send_nvim_command', '1'),
-        ('get_nvim_active_buffer', '2'),
-        ('get_nvim_cursor', '3'),
-        ('get_nvim_visual_selection', '4'),
-        ('set_nvim_diagnostics', '5'),
-        ('execute_nvim_lua', '6'),
-    ]
-
-    for func, old_id in funcs:
-        pattern = rf"let req = RmpValue::Array\(vec!\[\s*RmpValue::Integer\(0\.into\(\)\),\s*RmpValue::Integer\({old_id}\.into\(\)\), // msgid"
-        replacement = f"let msgid = NEXT_MSGID.fetch_add(1, Ordering::SeqCst);\n    let req = RmpValue::Array(vec![\n        RmpValue::Integer(0.into()),\n        RmpValue::Integer(msgid.into()), // msgid"
-        
-        content = re.sub(pattern, replacement, content)
-
-    with open(filepath, 'w', encoding='utf-8') as f:
-        f.write(content)
-
-    print('Fixed msgid allocations')
-
-fix_nvim_msgid()

server/src/fix_notes.py

@@ -1,40 +0,0 @@
-import os
-
-def fix_notes():
-    filepath = 'server/src/handlers_v2/notes.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    old_standup = """        let tasks = state
-            .tasks
-            .read()
-            .into_iter()
-            .filter(|t| t.updated_at >= cutoff)
-            .collect::<Vec<_>>();
-        let changes = state
-            .ledger
-            .read()
-            .into_iter()
-            .filter(|c| c.timestamp >= cutoff)
-            .collect::<Vec<_>>();
-        let summaries = state
-            .session_summaries
-            .read()
-            .into_iter()
-            .filter(|s| s.namespace == req.namespace && s.timestamp >= cutoff)
-            .collect::<Vec<_>>();"""
-
-    new_standup = """        let tasks = state.tasks.read_with(|items| items.iter().filter(|t| t.updated_at >= cutoff).cloned().collect::<Vec<_>>());
-        let changes = state.ledger.read_with(|items| items.iter().filter(|c| c.timestamp >= cutoff).cloned().collect::<Vec<_>>());
-        let summaries = state.session_summaries.read_with(|items| items.iter().filter(|s| s.namespace == req.namespace && s.timestamp >= cutoff).cloned().collect::<Vec<_>>());"""
-
-    if old_standup in content:
-        content = content.replace(old_standup, new_standup)
-        print('Replaced standup in notes.rs')
-    else:
-        print('Could not find old_standup in notes.rs')
-
-    with open(filepath, 'w', encoding='utf-8') as f:
-        f.write(content)
-
-fix_notes()

server/src/fix_stub.py

@@ -1,66 +0,0 @@
-import os
-
-def fix_stub_leaks():
-    filepath = 'stub/src/main.rs'
-    with open(filepath, 'r', encoding='utf-8') as f:
-        content = f.read()
-
-    # 1. Fix connect_async to handle shutdown and timeout
-    old_connect = """            match tokio_tungstenite::connect_async(request).await {"""
-    new_connect = """            let connect_result = tokio::select! {
-                _ = shutdown_rx.recv() => {
-                    tracing::info!("Shutdown received during connect");
-                    break;
-                }
-                res = tokio::time::timeout(
-                    tokio::time::Duration::from_secs(5),
-                    tokio_tungstenite::connect_async(request)
-                ) => res,
-            };
-
-            match connect_result {
-                Ok(Ok((ws_stream, _))) => {"""
-    
-    if old_connect in content:
-        content = content.replace(old_connect, new_connect)
-        print("Replaced connect_async")
-
-    # Fix Err block to match the new match structure
-    old_err = """                Err(e) => {
-                    tracing::error!("Failed to connect via WSS: {}", e);
-                    tokio::time::sleep(tokio::time::Duration::from_secs(1)).await;
-                }"""
-    new_err = """                Ok(Err(e)) => {
-                    tracing::error!("Failed to connect via WSS: {}", e);
-                    tokio::time::sleep(tokio::time::Duration::from_secs(1)).await;
-                }
-                Err(_) => {
-                    tracing::error!("Connection attempt timed out");
-                    tokio::time::sleep(tokio::time::Duration::from_secs(1)).await;
-                }"""
-    
-    if old_err in content:
-        content = content.replace(old_err, new_err)
-        print("Replaced Err branch")
-
-    # 2. Fix the break in send_task that exits the stub instead of reconnecting
-    old_select_send = """                        _ = &mut send_task => {
-                            tracing::error!("Send task exited");
-                            tokio::time::sleep(tokio::time::Duration::from_millis(50)).await;
-                            recv_task.abort();
-                            break;
-                        }"""
-    new_select_send = """                        _ = &mut send_task => {
-                            tracing::error!("Send task exited");
-                            tokio::time::sleep(tokio::time::Duration::from_millis(50)).await;
-                            recv_task.abort();
-                        }"""
-
-    if old_select_send in content:
-        content = content.replace(old_select_send, new_select_send)
-        print("Replaced select send_task")
-
-    with open(filepath, 'w', encoding='utf-8') as f:
-        f.write(content)
-
-fix_stub_leaks()

server/src/handlers.rs

@@ -1,197 +0,0 @@
-use crate::router::McpTool;
-use crate::state::MemoryState;
-use std::sync::Arc;
-
-pub struct MemoryHandler {
-    pub state: Arc<MemoryState>,
-    pub tools: std::collections::HashMap<String, Box<dyn McpTool>>,
-}
-
-impl MemoryHandler {
-    pub fn new(state: Arc<MemoryState>) -> Self {
-        let mut tools: std::collections::HashMap<String, Box<dyn McpTool>> =
-            std::collections::HashMap::new();
-
-        macro_rules! register {
-            ($module:ident::$handler:ident) => {
-                let h = crate::handlers_v2::$module::$handler;
-                tools.insert(h.name().to_string(), Box::new(h));
-            };
-        }
-
-        register!(graph::QueryGraphPathHandler);
-        register!(graph::CreateEntitiesHandler);
-        register!(graph::CreateRelationsHandler);
-        register!(graph::AddObservationsHandler);
-        register!(graph::DeleteEntitiesHandler);
-        register!(graph::DeleteObservationsHandler);
-        register!(graph::DeleteRelationsHandler);
-        register!(graph::ReadGraphHandler);
-        register!(graph::SearchNodesHandler);
-        register!(graph::OpenNodesHandler);
-        register!(graph::VisualizeGraphHandler);
-        register!(graph::CondenseEntityHandler);
-        register!(graph::MergeEntitiesHandler);
-        register!(graph::FindOrphansHandler);
-
-        register!(tasks::AddTaskHandler);
-        register!(tasks::DeleteTaskHandler);
-        register!(tasks::UpdateTaskStatusHandler);
-        register!(tasks::ListActiveTasksHandler);
-        register!(tasks::SetAcceptanceCriteriaHandler);
-        register!(tasks::VerifyAcceptanceCriteriaHandler);
-        register!(tasks::AddMilestoneHandler);
-        register!(tasks::UpdateMilestoneHandler);
-        register!(tasks::ListMilestonesHandler);
-
-        register!(notes::AddStickyNoteHandler);
-        register!(notes::ReadStickyNotesHandler);
-        register!(notes::DeleteStickyNoteHandler);
-        register!(notes::ClearStickyNotesHandler);
-        register!(notes::LeaveHandoffMemoHandler);
-        register!(notes::ReadHandoffMemosHandler);
-        register!(notes::ClearHandoffMemosHandler);
-        register!(notes::AddSessionSummaryHandler);
-        register!(notes::GenerateStandupReportHandler);
-
-        register!(meta::LogDecisionHandler);
-        register!(meta::QueryDecisionsHandler);
-        register!(meta::LogErrorFixHandler);
-        register!(meta::SearchErrorFixesHandler);
-        register!(meta::LogCodeChangeHandler);
-        register!(meta::QueryRecentChangesHandler);
-        register!(meta::LearnPreferenceHandler);
-        register!(meta::ReadPreferencesHandler);
-        register!(meta::LogTechDebtHandler);
-        register!(meta::ResolveTechDebtHandler);
-        register!(meta::ListTechDebtHandler);
-        register!(meta::OmniSearchHandler);
-        register!(meta::GetProjectHealthHandler);
-
-        register!(env::UpdateEnvFingerprintHandler);
-        register!(env::ReadEnvFingerprintHandler);
-        register!(env::LogEnvRequirementHandler);
-        register!(env::RegisterEnvironmentHandler);
-        register!(env::GetEnvironmentDetailsHandler);
-
-        register!(workspaces::PinFileHandler);
-        register!(workspaces::UnpinFileHandler);
-        register!(workspaces::ListPinnedFilesHandler);
-        register!(workspaces::StoreSnippetHandler);
-        register!(workspaces::SearchSnippetsHandler);
-        register!(workspaces::DeleteSnippetHandler);
-        register!(workspaces::SaveContextWorkspaceHandler);
-        register!(workspaces::LoadContextWorkspaceHandler);
-        register!(workspaces::ListContextWorkspacesHandler);
-        register!(workspaces::AddPrChecklistItemHandler);
-        register!(workspaces::GetPrChecklistHandler);
-        register!(workspaces::ClearPrChecklistHandler);
-
-        Self { state, tools }
-    }
-
-    pub async fn handle_request(&self, req: serde_json::Value) -> Option<serde_json::Value> {
-        let id = req.get("id").cloned().unwrap_or(serde_json::Value::Null);
-        let id_clone = id.clone();
-        let method = req.get("method").and_then(|m| m.as_str()).unwrap_or("");
-
-        match method {
-            "server/discover" => {
-                let payload = serde_json::json!({
-                    "resultType": "complete",
-                    "ttlMs": 0,
-                    "cacheScope": "public",
-                    "supportedVersions": ["2026-07-28", "2025-11-25", "2025-06-18", "2025-03-26", "2024-11-05"],
-                    "capabilities": {
-                        "tools": serde_json::json!({})
-                    },
-                    "_meta": {
-                        "io.modelcontextprotocol/serverInfo": {
-                            "name": "gemini-mcp-memory",
-                            "version": "3.0.0"
-                        }
-                    }
-                });
-                Some(crate::mcp::success(id, payload))
-            }
-            "initialize" => {
-                let init = rmcp::model::InitializeResult::new(
-                    rmcp::model::ServerCapabilities::builder()
-                        .enable_tools()
-                        .build(),
-                )
-                .with_server_info(rmcp::model::Implementation::new(
-                    "gemini-mcp-memory",
-                    "3.0.0",
-                ));
-                Some(crate::mcp::success(
-                    id,
-                    serde_json::to_value(&init).unwrap_or_default(),
-                ))
-            }
-            "notifications/initialized" => None,
-            "tools/list" => {
-                let mut tools: Vec<serde_json::Value> =
-                    self.tools.values().map(|t| t.schema()).collect();
-                tools.sort_by_key(|t| {
-                    t.get("name")
-                        .and_then(|n| n.as_str())
-                        .unwrap_or("")
-                        .to_string()
-                });
-                Some(crate::mcp::success(
-                    id,
-                    serde_json::json!({ "tools": tools }),
-                ))
-            }
-            "tools/call" => {
-                let params = req.get("params").unwrap_or(&serde_json::Value::Null);
-                let name = params.get("name").and_then(|n| n.as_str()).unwrap_or("");
-                let args = params
-                    .get("arguments")
-                    .cloned()
-                    .unwrap_or(serde_json::Value::Object(Default::default()));
-
-                self.state
-                    .broadcast_activity(&format!("Agent executed tool: {}", name));
-
-                let result: Result<String, String> = if let Some(tool) = self.tools.get(name) {
-                    tool.execute(args, self.state.clone()).await
-                } else {
-                    Err(format!("Unknown tool: {}", name))
-                };
-
-                match result {
-                    Ok(text) => {
-                        let payload = serde_json::json!({
-                            "content": [{"type": "text", "text": text}],
-                            "isError": false
-                        });
-                        Some(crate::mcp::success(id_clone, payload))
-                    }
-                    Err(e) => {
-                        tracing::error!("Tool {} failed: {}", name, e);
-                        let payload = serde_json::json!({
-                            "content": [{"type": "text", "text": e}],
-                            "isError": true
-                        });
-                        Some(crate::mcp::success(id_clone, payload))
-                    }
-                }
-            }
-            m if m.starts_with("notifications/") => None,
-            "ping" => Some(crate::mcp::success(id, serde_json::json!({}))),
-            _ => {
-                if id.is_null() {
-                    None
-                } else {
-                    Some(crate::mcp::error(
-                        id,
-                        -32601,
-                        &format!("Method {} not found", method),
-                    ))
-                }
-            }
-        }
-    }
-}

server/src/refactor.py

@@ -1,173 +0,0 @@
-import os
-import re
-
-GROUPS = {
-    "graph": [
-        "query_graph_path", "create_entities", "create_relations", "add_observations",
-        "delete_entities", "delete_observations", "delete_relations", "read_graph",
-        "search_nodes", "open_nodes", "visualize_graph", "condense_entity",
-        "merge_entities", "find_orphans"
-    ],
-    "tasks": [
-        "add_task", "delete_task", "update_task_status", "list_active_tasks",
-        "set_acceptance_criteria", "verify_acceptance_criteria",
-        "add_milestone", "update_milestone", "list_milestones"
-    ],
-    "notes": [
-        "add_sticky_note", "read_sticky_notes", "delete_sticky_note", "clear_sticky_notes",
-        "leave_handoff_memo", "read_handoff_memos", "clear_handoff_memos",
-        "add_session_summary", "generate_standup_report"
-    ],
-    "meta": [
-        "log_decision", "query_decisions", "log_error_fix", "search_error_fixes",
-        "log_code_change", "query_recent_changes", "learn_preference", "read_preferences",
-        "log_tech_debt", "resolve_tech_debt", "list_tech_debt", "omni_search", "get_project_health"
-    ],
-    "env": [
-        "update_env_fingerprint", "read_env_fingerprint", "log_env_requirement",
-        "register_environment", "get_environment_details"
-    ],
-    "workspaces": [
-        "pin_file", "unpin_file", "list_pinned_files", "store_snippet", "search_snippets",
-        "delete_snippet", "save_context_workspace", "load_context_workspace",
-        "list_context_workspaces", "add_pr_checklist_item", "get_pr_checklist", "clear_pr_checklist"
-    ]
-}
-
-def to_camel_case(snake_str):
-    components = snake_str.split('_')
-    return "".join(x.title() for x in components)
-
-def parse_rust_match(file_path):
-    with open(file_path, "r", encoding="utf-8") as f:
-        lines = f.readlines()
-        
-    start_idx = -1
-    for i, line in enumerate(lines):
-        if "let result: Result<String, String> = match name {" in line:
-            start_idx = i
-            break
-            
-    if start_idx == -1:
-        return {}
-        
-    brace_depth = 1
-    i = start_idx + 1
-    
-    tools = {}
-    current_tool = None
-    current_body = []
-    
-    while i < len(lines):
-        line = lines[i]
-        
-        if brace_depth == 1 and "=>" in line and '"' in line:
-            parts = line.strip().split('"')
-            if len(parts) >= 3:
-                tool_name = parts[1]
-                current_tool = tool_name
-                current_body = []
-                # Don't add the "name" => { line
-            
-        if current_tool is not None and not (brace_depth == 1 and "=>" in line and '"' in line):
-            # check if this line closes the block
-            next_depth = brace_depth + line.count('{') - line.count('}')
-            if next_depth == 1 and current_tool is not None:
-                # This is the closing brace
-                tools[current_tool] = "".join(current_body)
-                current_tool = None
-            else:
-                current_body.append(line)
-            
-        brace_depth += line.count('{')
-        brace_depth -= line.count('}')
-        
-        if brace_depth == 0:
-            break
-            
-        i += 1
-        
-    return tools
-
-def transform_body(body):
-    # Transform parse_tool!
-    body = re.sub(
-        r'let req = parse_tool!\(args, id, ([^)]+)\);',
-        r'let req: \1 = serde_json::from_value(args).map_err(|e| e.to_string())?;',
-        body
-    )
-    # Transform handle_list_with_namespace!
-    def repl_handle_list(m):
-        store = m.group(1)
-        tool_type = m.group(2)
-        return f"""
-        let req: {tool_type} = serde_json::from_value(args).map_err(|e| e.to_string())?;
-        let mut items = state.{store}.read();
-        if let Some(ns) = req.namespace {{
-            items.retain(|i| i.namespace == ns);
-        }}
-        let data = serde_json::to_string(&items).unwrap_or_default();
-        return Ok(data.to_string());
-        """
-    body = re.sub(
-        r'return handle_list_with_namespace!\(self, ([^,]+), ([^,]+), args, id\);',
-        repl_handle_list,
-        body
-    )
-    
-    # Replace self.state with state
-    body = body.replace("self.state.", "state.")
-    
-    return body
-
-
-tools = parse_rust_match("server/src/handlers.rs")
-
-for group, tool_names in GROUPS.items():
-    file_path = f"server/src/handlers_v2/{group}.rs"
-    with open(file_path, "w", encoding="utf-8") as f:
-        f.write("use crate::router::McpTool;\n")
-        f.write("use crate::state::MemoryState;\n")
-        f.write("use crate::tools::*;\n")
-        f.write("use async_trait::async_trait;\n")
-        f.write("use serde_json::Value;\n")
-        f.write("use std::sync::Arc;\n")
-        f.write("use std::time::{SystemTime, UNIX_EPOCH};\n\n")
-        
-        for name in tool_names:
-            if name not in tools:
-                continue
-            
-            body = tools[name]
-            # special case for query_graph_path which we already wrote properly?
-            # actually we will just overwrite it with the transformed body
-            body = transform_body(body)
-            
-            struct_name = to_camel_case(name) + "Handler"
-            tool_type = to_camel_case(name) + "Tool"
-            
-            f.write(f"pub struct {struct_name};\n\n")
-            f.write(f"#[async_trait]\n")
-            f.write(f"impl McpTool for {struct_name} {{\n")
-            f.write(f"    fn name(&self) -> &'static str {{\n")
-            f.write(f'        "{name}"\n')
-            f.write(f"    }}\n\n")
-            f.write(f"    fn schema(&self) -> Value {{\n")
-            # For schema description we can just put a generic one or extract it. 
-            # I will use a generic one for now, or you can extract it from tools/list.
-            f.write(f'        crate::mcp::tool_def::<{tool_type}>(\n')
-            f.write(f'            "{name}",\n')
-            f.write(f'            "Execute {name}",\n')
-            f.write(f'        )\n')
-            f.write(f"    }}\n\n")
-            f.write(f"    async fn execute(&self, args: Value, state: Arc<MemoryState>) -> Result<String, String> {{\n")
-            f.write(body)
-            f.write(f"    }}\n")
-            f.write(f"}}\n\n")
-
-print("Generated handlers_v2 modules")
-
-# generate mod.rs
-with open("server/src/handlers_v2/mod.rs", "w", encoding="utf-8") as f:
-    for group in GROUPS.keys():
-        f.write(f"pub mod {group};\n")

server/src/refactor.rs

@@ -1,11 +0,0 @@
-use std::fs;
-use std::io::Write;
-
-fn main() {
-    let content = fs::read_to_string("server/src/handlers.rs").unwrap();
-    println!("Read {} bytes", content.len());
-    // Find the match name { block
-    let match_start = content.find("match name {").unwrap();
-    // naive extraction
-    println!("Found match block at {}", match_start);
-}

server/src/refactor_router.py

@@ -1,82 +0,0 @@
-import re
-import os
-
-with open("server/src/handlers.rs", "r", encoding="utf-8") as f:
-    lines = f.readlines()
-
-list_start = -1
-for i, line in enumerate(lines):
-    if '"tools/list" => {' in line:
-        list_start = i
-        break
-
-# Find end of tools/call
-call_start = -1
-for i in range(list_start, len(lines)):
-    if '"tools/call" => {' in line:
-        call_start = i
-        break
-
-# Find end of tools/call
-# Match brace depth from call_start
-brace_depth = 1
-call_end = -1
-for i in range(call_start + 1, len(lines)):
-    brace_depth += lines[i].count('{')
-    brace_depth -= lines[i].count('}')
-    if brace_depth == 0:
-        call_end = i
-        break
-
-# replacement block
-replacement = """            "tools/list" => {
-                let mut tools: Vec<serde_json::Value> = self.tools.values().map(|t| t.schema()).collect();
-                tools.sort_by_key(|t| t.get("name").and_then(|n| n.as_str()).unwrap_or("").to_string());
-                Some(crate::mcp::success(
-                    id,
-                    serde_json::json!({ "tools": tools }),
-                ))
-            }
-            "tools/call" => {
-                let params = req.get("params").unwrap_or(&serde_json::Value::Null);
-                let name = params.get("name").and_then(|n| n.as_str()).unwrap_or("");
-                let args = params
-                    .get("arguments")
-                    .cloned()
-                    .unwrap_or(serde_json::Value::Object(Default::default()));
-
-                self.state
-                    .broadcast_activity(&format!("Agent executed tool: {}", name));
-
-                let result: Result<String, String> = if let Some(tool) = self.tools.get(name) {
-                    tool.execute(args, self.state.clone()).await
-                } else {
-                    Err(format!("Unknown tool: {}", name))
-                };
-
-                match result {
-                    Ok(text) => {
-                        let payload = serde_json::json!({
-                            "content": [{"type": "text", "text": text}],
-                            "isError": false
-                        });
-                        Some(crate::mcp::success(id_clone, payload))
-                    }
-                    Err(e) => {
-                        tracing::error!("Tool {} failed: {}", name, e);
-                        let payload = serde_json::json!({
-                            "content": [{"type": "text", "text": e}],
-                            "isError": true
-                        });
-                        Some(crate::mcp::success(id_clone, payload))
-                    }
-                }
-            }
-"""
-
-new_lines = lines[:list_start] + [replacement] + lines[call_end+1:]
-
-with open("server/src/handlers.rs", "w", encoding="utf-8") as f:
-    f.writelines(new_lines)
-
-print("tools/list and tools/call replaced.")

server/src/refactor_wire.py

@@ -1,106 +0,0 @@
-import re
-import os
-
-with open("server/src/handlers.rs", "r", encoding="utf-8") as f:
-    content = f.read()
-
-# Replace MemoryHandler struct
-struct_pattern = r'pub struct MemoryHandler \{\s*pub state: Arc<MemoryState>,\s*\}'
-
-new_struct = """use crate::router::McpTool;
-
-pub struct MemoryHandler {
-    pub state: Arc<MemoryState>,
-    pub tools: std::collections::HashMap<String, Box<dyn McpTool>>,
-}
-
-impl MemoryHandler {
-    pub fn new(state: Arc<MemoryState>) -> Self {
-        let mut tools: std::collections::HashMap<String, Box<dyn McpTool>> = std::collections::HashMap::new();
-        
-        macro_rules! register {
-            ($module:ident::$handler:ident) => {
-                let h = crate::handlers_v2::$module::$handler;
-                tools.insert(h.name().to_string(), Box::new(h));
-            };
-        }
-
-        register!(graph::QueryGraphPathHandler);
-        register!(graph::CreateEntitiesHandler);
-        register!(graph::CreateRelationsHandler);
-        register!(graph::AddObservationsHandler);
-        register!(graph::DeleteEntitiesHandler);
-        register!(graph::DeleteObservationsHandler);
-        register!(graph::DeleteRelationsHandler);
-        register!(graph::ReadGraphHandler);
-        register!(graph::SearchNodesHandler);
-        register!(graph::OpenNodesHandler);
-        register!(graph::VisualizeGraphHandler);
-        register!(graph::CondenseEntityHandler);
-        register!(graph::MergeEntitiesHandler);
-        register!(graph::FindOrphansHandler);
-
-        register!(tasks::AddTaskHandler);
-        register!(tasks::DeleteTaskHandler);
-        register!(tasks::UpdateTaskStatusHandler);
-        register!(tasks::ListActiveTasksHandler);
-        register!(tasks::SetAcceptanceCriteriaHandler);
-        register!(tasks::VerifyAcceptanceCriteriaHandler);
-        register!(tasks::AddMilestoneHandler);
-        register!(tasks::UpdateMilestoneHandler);
-        register!(tasks::ListMilestonesHandler);
-
-        register!(notes::AddStickyNoteHandler);
-        register!(notes::ReadStickyNotesHandler);
-        register!(notes::DeleteStickyNoteHandler);
-        register!(notes::ClearStickyNotesHandler);
-        register!(notes::LeaveHandoffMemoHandler);
-        register!(notes::ReadHandoffMemosHandler);
-        register!(notes::ClearHandoffMemosHandler);
-        register!(notes::AddSessionSummaryHandler);
-        register!(notes::GenerateStandupReportHandler);
-
-        register!(meta::LogDecisionHandler);
-        register!(meta::QueryDecisionsHandler);
-        register!(meta::LogErrorFixHandler);
-        register!(meta::SearchErrorFixesHandler);
-        register!(meta::LogCodeChangeHandler);
-        register!(meta::QueryRecentChangesHandler);
-        register!(meta::LearnPreferenceHandler);
-        register!(meta::ReadPreferencesHandler);
-        register!(meta::LogTechDebtHandler);
-        register!(meta::ResolveTechDebtHandler);
-        register!(meta::ListTechDebtHandler);
-        register!(meta::OmniSearchHandler);
-        register!(meta::GetProjectHealthHandler);
-
-        register!(env::UpdateEnvFingerprintHandler);
-        register!(env::ReadEnvFingerprintHandler);
-        register!(env::LogEnvRequirementHandler);
-        register!(env::RegisterEnvironmentHandler);
-        register!(env::GetEnvironmentDetailsHandler);
-
-        register!(workspaces::PinFileHandler);
-        register!(workspaces::UnpinFileHandler);
-        register!(workspaces::ListPinnedFilesHandler);
-        register!(workspaces::StoreSnippetHandler);
-        register!(workspaces::SearchSnippetsHandler);
-        register!(workspaces::DeleteSnippetHandler);
-        register!(workspaces::SaveContextWorkspaceHandler);
-        register!(workspaces::LoadContextWorkspaceHandler);
-        register!(workspaces::ListContextWorkspacesHandler);
-        register!(workspaces::AddPrChecklistItemHandler);
-        register!(workspaces::GetPrChecklistHandler);
-        register!(workspaces::ClearPrChecklistHandler);
-
-        Self { state, tools }
-    }
-"""
-
-content = re.sub(struct_pattern, new_struct, content)
-content = content.replace("impl MemoryHandler {\n    pub async fn handle_request", "    pub async fn handle_request")
-
-with open("server/src/handlers.rs", "w", encoding="utf-8") as f:
-    f.write(content)
-
-print("MemoryHandler struct updated.")

server/src/tools_patch.rs

@@ -1,45 +0,0 @@
-use schemars::JsonSchema;
-use serde::{Deserialize, Serialize};
-
-/// Create new entities in the knowledge graph.
-#[derive(Debug, Deserialize, Serialize, JsonSchema)]
-pub struct CreateEntitiesTool {
-    pub entities: Vec<crate::models::Entity>,
-}
-
-/// Create new relations between entities in the knowledge graph.
-#[derive(Debug, Deserialize, Serialize, JsonSchema)]
-pub struct CreateRelationsTool {
-    pub relations: Vec<crate::models::Relation>,
-}
-
-#[derive(Debug, Deserialize, Serialize, JsonSchema)]
-pub struct ObservationInput {
-    #[serde(rename = "entityName")]
-    pub entity_name: String,
-    pub contents: Vec<String>,
-}
-
-/// Add new observations to existing entities in the knowledge graph.
-#[derive(Debug, Deserialize, Serialize, JsonSchema)]
-pub struct AddObservationsTool {
-    pub observations: Vec<ObservationInput>,
-}
-
-/// Define a strict checklist of acceptance criteria for a given task or feature before starting work.
-#[derive(Debug, Deserialize, Serialize, JsonSchema)]
-pub struct SetAcceptanceCriteriaTool {
-    /// The name or title of the task/feature being worked on.
-    pub task_title: String,
-    /// An array of specific, undeniable conditions that must be proven before claiming success.
-    pub criteria: Vec<String>,
-}
-
-/// Mark a previously defined acceptance criteria as met by providing cryptographic-like proof (logs, output, diffs).
-#[derive(Debug, Deserialize, Serialize, JsonSchema)]
-pub struct VerifyAcceptanceCriteriaTool {
-    /// The exact text of the criteria being met.
-    pub criteria: String,
-    /// The undeniable proof (e.g., test logs, terminal output, git diff) that proves the criteria is met.
-    pub proof: String,
-}

server/update_win_config.py

@@ -1,37 +0,0 @@
-import json
-import os
-
-eager_tools = [
-    "log_code_change",
-    "log_error_fix",
-    "log_tech_debt",
-    "omni_search",
-    "create_entities",
-    "learn_preference",
-    "list_active_tasks",
-    "add_task",
-    "set_acceptance_criteria",
-    "verify_acceptance_criteria",
-    "update_task_status",
-    "list_pinned_files",
-    "pin_file",
-    "unpin_file",
-    "get_project_health",
-    "list_tech_debt",
-    "resolve_tech_debt"
-]
-
-# Update Windows config
-win_config_path = r'C:\Users\reazul.ashraf\.gemini\config\mcp_config.json'
-with open(win_config_path, 'r', encoding='utf-8') as f:
-    win_data = json.load(f)
-
-win_data['mcpServers']['mcp-memory']['eagerTools'] = eager_tools
-if 'args' in win_data['mcpServers']['mcp-memory']:
-    # Ensure args are empty as we removed --target earlier
-    win_data['mcpServers']['mcp-memory']['args'] = []
-
-with open(win_config_path, 'w', encoding='utf-8') as f:
-    json.dump(win_data, f, indent=2)
-
-print("Updated Windows config")

temp.lua

@@ -1,27 +0,0 @@
-local buf = vim.fn.bufnr('server/src/search.rs')
-if buf == -1 then
-    vim.cmd('e server/src/search.rs')
-    buf = vim.api.nvim_get_current_buf()
-end
-
-vim.api.nvim_buf_set_lines(buf, 216, 222, false, {
-    '        &self,',
-    '        entities: &[Entity],',
-    '        tasks: &[Task],',
-    '        snippets: &[Snippet],',
-    '        adrs: &[Adr],'
-})
-
--- We need to change the loop variables inside the task from values to clones if they are passed as slices
--- Actually we can just clone the slice data before moving it into spawn_blocking
-vim.api.nvim_buf_set_lines(buf, 222, 223, false, {
-    '    ) -> tokio::task::JoinHandle<tantivy::Result<()>> {',
-    '        let entities = entities.to_vec();',
-    '        let tasks = tasks.to_vec();',
-    '        let snippets = snippets.to_vec();',
-    '        let adrs = adrs.to_vec();'
-})
-
-vim.cmd('write')
-require('notify')('Updated search index_batch signature', 'info', { title = 'Antigravity' })
-return 'ok'

temp_execute.lua

@@ -1,28 +0,0 @@
-local buf = vim.fn.bufnr('server/src/search.rs')
-if buf == -1 then
-    vim.cmd('e server/src/search.rs')
-    buf = vim.api.nvim_get_current_buf()
-end
-
-vim.api.nvim_buf_set_lines(buf, 216, 222, false, {
-    '        &self,',
-    '        entities: &[Entity],',
-    '        tasks: &[Task],',
-    '        snippets: &[Snippet],',
-    '        adrs: &[Adr],'
-})
-
--- We need to change the loop variables inside the task from values to clones if they are passed as slices
--- Actually we can just clone the slice data before moving it into spawn_blocking
-vim.api.nvim_buf_set_lines(buf, 222, 223, false, {
-    '    ) -> tokio::task::JoinHandle<tantivy::Result<()>> {',
-    '        let entities = entities.to_vec();',
-    '        let tasks = tasks.to_vec();',
-    '        let snippets = snippets.to_vec();',
-    '        let adrs = adrs.to_vec();'
-})
-
-vim.cmd('write')
-require('notify')('Updated search index_batch signature', 'info', { title = 'Antigravity' })
-return 'ok'
-

temp_read.lua

@@ -1,2 +0,0 @@
-local code = vim.fn.readfile('temp.lua')
-return table.concat(code, '\n')

temp_setup.lua

@@ -1,6 +0,0 @@
-local buf = vim.fn.bufnr('server/src/handlers_v2/graph.rs')
-if buf == -1 then
-    vim.cmd('e server/src/handlers_v2/graph.rs')
-    buf = vim.api.nvim_get_current_buf()
-end
-return vim.api.nvim_buf_get_name(buf)

update_main.patch

@@ -1,25 +0,0 @@
---- server/src/main.rs
-+++ server/src/main.rs
-@@ -225,6 +225,20 @@
-         next_id: AtomicUsize::new(1),
-     });
- 
-+    let app_state_clone = Arc::clone(&app_state);
-+    let mut rx = state.activity_tx.subscribe();
-+    tokio::spawn(async move {
-+        while let Ok(msg) = rx.recv().await {
-+            let senders: Vec<_> = app_state_clone
-+                .clients
-+                .read()
-+                .unwrap_or_else(|e| e.into_inner())
-+                .values()
-+                .cloned()
-+                .collect();
-+            for client_tx in senders {
-+                let _ = client_tx.try_send(msg.clone());
-+            }
-+        }
-+    });
-+
-     let app = Router::new()
-             .route(