Merge pull request #21 from devwhodevs/feat/v1.5.5-housekeeping

v1.5.5: rmcp 1.4, auto_link parameter, reindex_file tool

Author: devwhodevs

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## v1.5.5 — Housekeeping (2026-04-10)
+
+### Added
+- **`auto_link` parameter** on `create` — set to `false` to skip automatic wikilink resolution. Applies to MCP, HTTP, and CLI. Discovered links still appear as suggestions in the response.
+- **`reindex_file` MCP tool + HTTP endpoint** — re-indexes a single file after external edits. Reads from disk, re-embeds chunks, rebuilds edges. Available as MCP tool, `POST /api/reindex-file`, and OpenAPI operation.
+
+### Changed
+- **rmcp** bumped from 1.2.0 to 1.4.0 — host validation, non-Send handler support, transport fixes. Does not yet fix [#20](https://github.com/devwhodevs/engraph/issues/20) (protocol `2025-11-25` needed for Claude Desktop Cowork/Code modes — blocked upstream on [modelcontextprotocol/rust-sdk#800](https://github.com/modelcontextprotocol/rust-sdk/issues/800)).
+- MCP tools: 22 → 23
+- HTTP endpoints: 23 → 24
+- OpenAPI version: 1.5.0 → 1.5.5
+
 ## v1.5.0 — ChatGPT Actions (2026-03-26)
 
 ### Added

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name = "engraph"
-version = "1.5.4"
+version = "1.5.5"
 edition = "2024"
 description = "Local knowledge graph for AI agents. Hybrid search + MCP server for Obsidian vaults."
 license = "MIT"
@@ -31,7 +31,7 @@ rayon = "1"
 time = { version = "0.3", features = ["parsing", "formatting", "macros"] }
 strsim = "0.11"
 ignore = "0.4"
-rmcp = { version = "1.2", features = ["transport-io"] }
+rmcp = { version = "1.4", features = ["transport-io"] }
 tokio = { version = "1", features = ["macros", "rt-multi-thread", "process", "time", "net"] }
 notify = "7.0"
 notify-debouncer-full = "0.4"

Cargo.toml

@@ -268,7 +268,7 @@ Returns orphan notes (no links in or out), broken wikilinks, stale notes, and ta
 
 `engraph serve --http` adds a full REST API alongside the MCP server, exposing the same capabilities over HTTP for web agents, scripts, and integrations.
 
-**23 endpoints:**
+**24 endpoints:**
 
 | Method | Endpoint | Permission | Description |
 |--------|----------|------------|-------------|
@@ -292,6 +292,7 @@ Returns orphan notes (no links in or out), broken wikilinks, stale notes, and ta
 | POST | `/api/unarchive` | write | Restore archived note |
 | POST | `/api/update-metadata` | write | Update note metadata |
 | POST | `/api/delete` | write | Delete note (soft or hard) |
+| POST | `/api/reindex-file` | write | Re-index a single file after external edits |
 | POST | `/api/migrate/preview` | write | Preview PARA migration (classify + suggest moves) |
 | POST | `/api/migrate/apply` | write | Apply PARA migration (move files) |
 | POST | `/api/migrate/undo` | write | Undo last PARA migration |
@@ -542,8 +543,8 @@ engraph is not a replacement for Obsidian — it's the intelligence layer that s
 - LLM research orchestrator: query intent classification + query expansion + adaptive lane weights
 - llama.cpp inference via Rust bindings (GGUF models, Metal GPU on macOS, CUDA on Linux)
 - Intelligence opt-in: heuristic fallback when disabled, LLM-powered when enabled
-- MCP server with 22 tools (8 read, 10 write, 1 diagnostic, 3 migrate) via stdio
-- HTTP REST API with 23 endpoints, API key auth (`eg_` prefix), rate limiting, CORS — enabled via `engraph serve --http`
+- MCP server with 23 tools (8 read, 10 write, 1 index, 1 diagnostic, 3 migrate) via stdio
+- HTTP REST API with 24 endpoints, API key auth (`eg_` prefix), rate limiting, CORS — enabled via `engraph serve --http`
 - Section-level reading and editing: target specific headings with replace/prepend/append modes
 - Full note rewriting with automatic frontmatter preservation
 - Granular frontmatter mutations: set/remove fields, add/remove tags and aliases
@@ -572,7 +573,9 @@ engraph is not a replacement for Obsidian — it's the intelligence layer that s
 - [x] ~~HTTP/REST API — complement MCP with a standard web API~~ (v1.3)
 - [x] ~~PARA migration — AI-assisted vault restructuring with preview/apply/undo~~ (v1.4)
 - [x] ~~ChatGPT Actions — OpenAPI 3.1.0 spec + plugin manifest + `--setup-chatgpt` helper~~ (v1.5)
-- [ ] Multi-vault — search across multiple vaults (v1.6)
+- [ ] Identity — user context at session start, enhanced onboarding (v1.6)
+- [ ] Timeline — temporal knowledge graph with point-in-time queries (v1.7)
+- [ ] Mining — automatic fact extraction from vault notes (v1.8)
 
 ## Configuration
 

README.md

@@ -268,6 +268,7 @@ struct CreateBody {
     #[serde(default)]
     tags: Vec<String>,
     folder: Option<String>,
+    auto_link: Option<bool>,
 }
 
 #[derive(Debug, Deserialize)]
@@ -326,6 +327,11 @@ struct DeleteBody {
     mode: Option<String>,
 }
 
+#[derive(Debug, Deserialize)]
+struct ReindexFileBody {
+    file: String,
+}
+
 // ---------------------------------------------------------------------------
 // CORS
 // ---------------------------------------------------------------------------
@@ -380,6 +386,8 @@ pub fn build_router(state: ApiState) -> Router {
         .route("/api/unarchive", post(handle_unarchive))
         .route("/api/update-metadata", post(handle_update_metadata))
         .route("/api/delete", post(handle_delete))
+        // Index maintenance
+        .route("/api/reindex-file", post(handle_reindex_file))
         // Migration endpoints
         .route("/api/migrate/preview", post(handle_migrate_preview))
         .route("/api/migrate/apply", post(handle_migrate_apply))
@@ -712,6 +720,7 @@ async fn handle_create(
         tags: body.tags,
         folder: body.folder,
         created_by: "http-api".into(),
+        auto_link: body.auto_link,
     };
     let result = writer::create_note(
         input,
@@ -1011,6 +1020,52 @@ async fn handle_delete(
     })))
 }
 
+async fn handle_reindex_file(
+    State(state): State<ApiState>,
+    headers: HeaderMap,
+    Json(body): Json<ReindexFileBody>,
+) -> Result<impl IntoResponse, ApiError> {
+    authorize(&headers, &state, true)?;
+    let store = state.store.lock().await;
+    let mut embedder = state.embedder.lock().await;
+    let full_path = state.vault_path.join(&body.file);
+
+    let content = std::fs::read_to_string(&full_path)
+        .map_err(|e| ApiError::internal(&format!("Cannot read file {}: {e}", body.file)))?;
+
+    let content_hash = {
+        use sha2::{Digest, Sha256};
+        let mut hasher = Sha256::new();
+        hasher.update(content.as_bytes());
+        format!("{:x}", hasher.finalize())
+    };
+
+    let config = crate::config::Config::load().unwrap_or_default();
+
+    let result = crate::indexer::index_file(
+        &body.file,
+        &content,
+        &content_hash,
+        &store,
+        &mut *embedder,
+        &state.vault_path,
+        &config,
+    )
+    .map_err(|e| ApiError::internal(&format!("{e:#}")))?;
+
+    store
+        .delete_edges_for_file(result.file_id)
+        .map_err(|e| ApiError::internal(&format!("{e:#}")))?;
+    crate::indexer::build_edges_for_file(&store, result.file_id, &content)
+        .map_err(|e| ApiError::internal(&format!("{e:#}")))?;
+
+    Ok(Json(serde_json::json!({
+        "file": body.file,
+        "chunks": result.total_chunks,
+        "docid": result.docid,
+    })))
+}
+
 // ---------------------------------------------------------------------------
 // Tests
 // ---------------------------------------------------------------------------

src/http.rs

@@ -1280,6 +1280,7 @@ async fn main() -> Result<()> {
                         tags,
                         folder,
                         created_by: "cli".into(),
+                        auto_link: None,
                     };
                     let result = engraph::writer::create_note(
                         input,

src/main.rs

@@ -27,6 +27,7 @@ pub fn build_openapi_spec(server_url: &str) -> serde_json::Value {
     paths.insert("/api/unarchive".into(), build_unarchive());
     paths.insert("/api/update-metadata".into(), build_update_metadata());
     paths.insert("/api/delete".into(), build_delete());
+    paths.insert("/api/reindex-file".into(), build_reindex_file());
 
     // Migration endpoints
     paths.insert("/api/migrate/preview".into(), build_migrate_preview());
@@ -37,7 +38,7 @@ pub fn build_openapi_spec(server_url: &str) -> serde_json::Value {
         "openapi": "3.1.0",
         "info": {
             "title": "engraph",
-            "version": "1.5.0",
+            "version": "1.5.5",
             "description": "AI-powered semantic search and management API for Obsidian vaults."
         },
         "servers": [{ "url": server_url }],
@@ -220,7 +221,8 @@ fn build_create() -> serde_json::Value {
                         "filename": { "type": "string", "description": "Filename without .md" },
                         "type_hint": { "type": "string", "description": "Type hint for placement" },
                         "tags": { "type": "array", "items": { "type": "string" }, "description": "Tags to apply" },
-                        "folder": { "type": "string", "description": "Explicit folder (skips auto-placement)" }
+                        "folder": { "type": "string", "description": "Explicit folder (skips auto-placement)" },
+                        "auto_link": { "type": "boolean", "description": "Set to false to skip automatic wikilink resolution. Defaults to true." }
                     }
                 }}}
             },
@@ -428,6 +430,26 @@ fn build_delete() -> serde_json::Value {
     })
 }
 
+fn build_reindex_file() -> serde_json::Value {
+    serde_json::json!({
+        "post": {
+            "operationId": "reindexFile",
+            "summary": "Re-index a single file after external edits. Re-reads, re-embeds, and updates search index.",
+            "requestBody": {
+                "required": true,
+                "content": { "application/json": { "schema": {
+                    "type": "object",
+                    "required": ["file"],
+                    "properties": {
+                        "file": { "type": "string", "description": "File path relative to vault root" }
+                    }
+                }}}
+            },
+            "responses": { "200": { "description": "Re-indexed file info (chunks, docid)" } }
+        }
+    })
+}
+
 fn build_migrate_preview() -> serde_json::Value {
     serde_json::json!({
         "post": {

src/openapi.rs

@@ -83,6 +83,8 @@ pub struct CreateParams {
     pub tags: Option<Vec<String>>,
     /// Explicit folder path (skips placement engine).
     pub folder: Option<String>,
+    /// Set to false to skip automatic wikilink resolution. Defaults to true.
+    pub auto_link: Option<bool>,
 }
 
 #[derive(Debug, Deserialize, JsonSchema)]
@@ -184,6 +186,12 @@ pub struct DeleteParams {
     pub mode: Option<String>,
 }
 
+#[derive(Debug, Deserialize, JsonSchema)]
+pub struct ReindexFileParams {
+    /// File path relative to vault root (e.g. "07-Daily/2026-04-10.md").
+    pub file: String,
+}
+
 // ---------------------------------------------------------------------------
 // Server
 // ---------------------------------------------------------------------------
@@ -198,6 +206,7 @@ pub struct EngraphServer {
     embedder: Arc<Mutex<Box<dyn EmbedModel + Send>>>,
     vault_path: Arc<PathBuf>,
     profile: Arc<Option<VaultProfile>>,
+    #[allow(dead_code)] // Required by rmcp #[tool_router] macro infrastructure
     tool_router: ToolRouter<Self>,
     /// Query expansion orchestrator (None when intelligence is disabled or failed to load).
     orchestrator: Option<Arc<Mutex<Box<dyn OrchestratorModel + Send>>>>,
@@ -512,6 +521,7 @@ impl EngraphServer {
             tags: params.0.tags.unwrap_or_default(),
             folder: params.0.folder,
             created_by: "claude-code".into(),
+            auto_link: params.0.auto_link,
         };
         let result = crate::writer::create_note(
             input,
@@ -818,6 +828,64 @@ impl EngraphServer {
         });
         to_json_result(&result)
     }
+
+    #[tool(
+        name = "reindex_file",
+        description = "Re-index a single file after external edits. Reads the file from disk, re-embeds its chunks, and updates the search index. Use when a file was modified outside engraph and you need the index to reflect current content."
+    )]
+    async fn reindex_file(
+        &self,
+        params: Parameters<ReindexFileParams>,
+    ) -> Result<CallToolResult, McpError> {
+        let store = self.store.lock().await;
+        let mut embedder = self.embedder.lock().await;
+        let rel_path = params.0.file;
+        let full_path = self.vault_path.join(&rel_path);
+
+        // Read file content from disk
+        let content = std::fs::read_to_string(&full_path).map_err(|e| {
+            McpError::new(
+                rmcp::model::ErrorCode::INVALID_PARAMS,
+                format!("Cannot read file {rel_path}: {e}"),
+                None::<serde_json::Value>,
+            )
+        })?;
+
+        let content_hash = {
+            use sha2::{Digest, Sha256};
+            let mut hasher = Sha256::new();
+            hasher.update(content.as_bytes());
+            format!("{:x}", hasher.finalize())
+        };
+
+        let config = crate::config::Config::load().unwrap_or_default();
+
+        // Re-index the file (handles cleanup of old entries automatically)
+        let result = crate::indexer::index_file(
+            &rel_path,
+            &content,
+            &content_hash,
+            &store,
+            &mut *embedder,
+            &self.vault_path,
+            &config,
+        )
+        .map_err(|e| mcp_err(&e))?;
+
+        // Rebuild edges for the re-indexed file
+        store
+            .delete_edges_for_file(result.file_id)
+            .map_err(|e| mcp_err(&e))?;
+        crate::indexer::build_edges_for_file(&store, result.file_id, &content)
+            .map_err(|e| mcp_err(&e))?;
+
+        let output = serde_json::json!({
+            "file": rel_path,
+            "chunks": result.total_chunks,
+            "docid": result.docid,
+        });
+        to_json_result(&output)
+    }
 }
 
 #[tool_handler]
@@ -829,6 +897,7 @@ impl rmcp::handler::server::ServerHandler for EngraphServer {
                  Write: create for new notes, append to add content, edit to modify a section, rewrite to replace body, \
                  edit_frontmatter for tags/properties, update_metadata for bulk tag/alias replacement. \
                  Lifecycle: move_note to relocate, archive to soft-delete, unarchive to restore, delete for permanent removal. \
+                 Index: reindex_file to refresh a single file's index after external edits. \
                  Migration: migrate_preview to classify notes into PARA folders, migrate_apply to execute the migration, migrate_undo to revert.",
         )
     }