rubien-mcp-server 0.1.0 → 0.3.0

package/README.md

@@ -1,179 +1,177 @@
 # rubien-mcp-server
 
-A Model Context Protocol server that wraps `rubien-cli`, making the Rubien reference library available to Claude Code, Claude Desktop, and claude.ai chat as a callable tool catalog.
+A Model Context Protocol server that wraps `rubien-cli`, exposing your Rubien library to Claude Code, Claude Desktop, and claude.ai (web) as a tool catalog. It spawns `rubien-cli` under the hood and speaks MCP over two transports:
 
-The server is a thin Node/TypeScript process. It spawns `rubien-cli` under the hood and speaks MCP over one of two transports:
+- **stdio** — Claude Code and Claude Desktop. The client spawns the server locally. No network, no auth. What most people want; see [Install](#install).
+- **Streamable HTTP + bearer token** — claude.ai (web) connects as a *remote MCP server* (it can't spawn a local process), so it needs a tunnel. See [claude.ai web](#claudeai-web-remote-mcp-server).
 
-- **stdio** — used by **Claude Code** and **Claude Desktop**. The client launches the server as a child process and talks to it over the pipe. No network, no auth.
-- **Streamable HTTP with bearer-token auth** — used by **claude.ai (web)** via a custom MCP connector. Requires a tunnel (e.g. Cloudflare Tunnel) because your library lives on your Mac.
+## Requirement: `rubien-cli` on the host
 
-Pick the section below that matches your client. Most users want one of the two stdio paths.
+The server is only a wrapper. It needs **Node.js ≥ 20** and the `rubien-cli` binary:
 
-## Install (Claude Code)
+- **Mac:** install **Rubien.app** (the DMG). The entitled `rubien-cli` ships inside it and is found automatically.
+- **Linux:** install the runtime libs and extract the CLI tarball, keeping `rubien-cli` and its `*.resources` folders together (the CLI loads citation styles from beside the binary):
+  ```bash
+  sudo apt install libsqlite3-0 libcurl4 libxml2 libpoppler-glib8 libcairo2 libgdk-pixbuf-2.0-0 libglib2.0-0 ca-certificates
+  # download rubien-cli-*-linux-x86_64.tar.gz, extract, then:
+  export RUBIEN_CLI=/path/to/extracted/rubien-cli
+  ```
+  Tarball: <https://github.com/devzhk/Rubien-releases/releases>. Don't put the bare binary on `PATH` alone — it loses its resource bundles.
 
-```bash
-claude mcp add rubien -- npx -y rubien-mcp-server
-```
-
-This needs `rubien-cli` on the host:
-- **Mac:** install Rubien.app (DMG) — the entitled `rubien-cli` ships inside it; nothing else to do.
-- **Linux:** `sudo apt install libsqlite3-0 libcurl4 libxml2 libpoppler-glib8 libcairo2 libgdk-pixbuf-2.0-0 libglib2.0-0 ca-certificates`, then download `rubien-cli-*-linux-x86_64.tar.gz` from
-  https://github.com/devzhk/Rubien-releases/releases and **extract it to a directory, keeping `rubien-cli` and the `*.resources` folders together** (the CLI loads citation styles from beside the binary). Point the server at it: `export RUBIEN_CLI=/path/to/extracted/rubien-cli`. Do **not** copy the bare binary onto `PATH` alone — it would lose its resource bundles.
-
-The server checks the CLI's build at startup; if it's too old it prints an update
-instruction and exits (rather than failing mid-call). On **Mac**, update Rubien.app
-(Sparkle). On **Linux**, run `rubien-cli self-update` (signature-verified, replaces in
-place) — or re-download the tarball.
-
-## Prerequisites
+At startup the server checks the CLI's build and exits with an update instruction if it's too old. Update via Rubien.app / Sparkle on Mac, or `rubien-cli self-update` on Linux.
 
-- Node.js ≥ 20
-- `rubien-cli` reachable on the host. The server looks for it in this order:
-  1. `$RUBIEN_CLI` env var (explicit path)
-  2. `/Applications/Rubien.app/Contents/Helpers/rubien-cli` (installed app bundle, Mac)
-  3. `~/Applications/Rubien.app/Contents/Helpers/rubien-cli` (Mac)
-  4. `./build/Rubien.app/Contents/Helpers/rubien-cli` (dev build output, Mac)
-  5. `rubien-cli` on `PATH` (Linux installs land here — see the **Install** section above)
+## Install
 
-**On Mac, prefer the bundled helper.** It's signed with the App Group entitlement and reads the same `library.sqlite` the Rubien app uses. A bare `rubien-cli` on PATH is typically an SPM dev build without the entitlement, which hits a *different* database — see "Database location" in `Docs/CLI-Reference.md`.
+Both stdio clients use the published npm package via `npx -y` — no global install.
 
-**On Linux**, the server runs against a `rubien-cli` installed per the **Install** section above (prebuilt Linux tarball, or built from source). Everything works except `rubien_sync_status`, which always errors (`sync` subcommand isn't registered on Linux builds — CloudKit doesn't exist there).
-
-To pin the spawned CLI to a specific library directory regardless of which binary resolves, set `RUBIEN_LIBRARY_ROOT` in the MCP server's `env` block (Claude Code: `claude mcp add rubien --env RUBIEN_LIBRARY_ROOT=...`; Claude Desktop: under `mcpServers.rubien.env` in `claude_desktop_config.json`). The path is used verbatim — point it at the directory that contains `library.sqlite`:
-
-- Mac sandboxed: `~/Library/Group Containers/9TXK4V3SS8.com.rubien.shared/Rubien`
-- Mac unsandboxed: `~/Library/Application Support/Rubien`
-- Linux: `~/.local/share/rubien` (or wherever `$XDG_DATA_HOME/rubien` resolved to)
-
-## Claude Code (stdio)
-
-The npx command above is the recommended path. To run a local checkout instead (see [Development](#development) for the build):
+### Claude Code
 
 ```bash
-claude mcp add rubien node $(pwd)/dist/index.js
+claude mcp add rubien -- npx -y rubien-mcp-server
 ```
 
-Try it:
-
-> List my 5 most recently added references.
-> Cite reference 42 in Nature style.
+### Claude Desktop
 
-Claude Code's permission UI prompts for the destructive tools (`rubien_delete`, `rubien_update`, `rubien_import`, and the property write tools) on first use.
-
-## Claude Desktop (stdio)
-
-Claude Desktop spawns MCP servers itself — no tunnel, no bearer token. Add Rubien to `claude_desktop_config.json` via either route:
-
-- **Edit the file directly** at `~/Library/Application Support/Claude/claude_desktop_config.json`.
-- **Settings → Developer → Edit Config** in Claude Desktop, which opens the same file in your editor.
-
-Add Rubien under `mcpServers`:
+**Settings → Developer → Edit Config** (or edit `~/Library/Application Support/Claude/claude_desktop_config.json`), then restart Claude Desktop:
 
 ```json
 {
   "mcpServers": {
     "rubien": {
-      "command": "node",
-      "args": ["/absolute/path/to/Rubien/mcp-server/dist/index.js"]
+      "command": "npx",
+      "args": ["-y", "rubien-mcp-server"]
     }
   }
 }
 ```
 
-Restart Claude Desktop and Rubien appears in the tool picker. To pin the spawned CLI to a specific library (see *Prerequisites* above for paths), add an `env` block:
+**macOS PATH gotcha:** Claude Desktop launches servers with launchd's minimal `PATH`, not your shell's. If `npx` isn't found, set `"command"` to its absolute path (`which npx` → e.g. `/opt/homebrew/bin/npx`). Affects every npx-based server; Claude Code is unaffected. No `.dxt` one-click package yet.
 
-```json
-"rubien": {
-  "command": "node",
-  "args": ["/absolute/path/to/Rubien/mcp-server/dist/index.js"],
-  "env": {
-    "RUBIEN_LIBRARY_ROOT": "/Users/you/Library/Group Containers/9TXK4V3SS8.com.rubien.shared/Rubien"
-  }
-}
-```
+### Upgrading
+
+The `npx -y rubien-mcp-server` install is **unpinned**, so there is nothing to reinstall — `npx` resolves the latest published version each time the client spawns the server. Upgrade in this order:
 
-> **Future work — Desktop Extension (`.dxt`).** Claude Desktop also supports one-click MCP installs via `.dxt` packages (a zip containing a `manifest.json` + bundled server). Rubien doesn't ship one yet; packaging it would replace the config-file edit above with a double-click install from a GitHub Release asset.
+1. **Update Rubien first** — Sparkle on Mac (Rubien → Settings → Check Now), `rubien-cli self-update` on Linux. The server needs the new `rubien-cli`.
+2. **Restart your MCP client** — quit/reopen Claude Desktop, or start a new Claude Code session. The respawned server is the latest release.
 
-## claude.ai web (Streamable HTTP + Cloudflare Tunnel)
+The pairing is guarded in one direction: a new server against a too-old Rubien **exits at startup with an update instruction** (`MIN_CLI_BUILD`), so a half-upgrade fails fast instead of half-working. The other direction is why upgrading matters — an old server against a new Rubien breaks at tool-call time when it shells subcommands that no longer exist (server < 0.3.0 vs Rubien ≥ 0.4.0: the 0.4.0 CLI cutover removed `import`, `add --identifier`, `views --query`, and the legacy `properties` write flags that 0.1.x/0.2.x servers shell out to; those server versions are deprecated on npm for this reason).
 
-claude.ai (the web app at https://claude.ai) can't spawn a local process, so it talks to the server over HTTPS via a custom MCP connector. Since your library lives on your Mac, you'll need a tunnel to expose the local server, and bearer-token auth to keep strangers out.
+If a stale `npx` cache ever keeps serving an old version after a restart, clear it (`rm -rf ~/.npm/_npx`) or pin `rubien-mcp-server@latest` in the config. HTTP mode (below) runs as a long-lived process you started yourself — it does not auto-upgrade; restart it after updating Rubien.
+
+## claude.ai web (remote MCP server)
+
+claude.ai connects to rubien as a **remote MCP server** over Streamable HTTP — it can't spawn a local process. It's the *same npm package* in HTTP mode: the server still runs on your Mac (where the library and `rubien-cli` live), and claude.ai reaches it through a Cloudflare Tunnel, with a bearer token to keep strangers out.
 
 ```bash
-# 1. Start the server with a bearer token
+# 1. Start the server in HTTP mode with a bearer token
 RUBIEN_MCP_BEARER=$(openssl rand -hex 32) \
-  node dist/index.js --http --port 4000 --bearer-token "$RUBIEN_MCP_BEARER"
+  npx -y rubien-mcp-server --http --port 4000 --bearer-token "$RUBIEN_MCP_BEARER"
 
 # 2. Open a tunnel
 cloudflared tunnel --url http://localhost:4000
 # → copy the https://*.trycloudflare.com URL
 
-# 3. In claude.ai: Settings → Connectors → Add custom MCP connector
-#    URL:   https://<your-tunnel>.trycloudflare.com
-#    Token: $RUBIEN_MCP_BEARER (from step 1)
+# 3. claude.ai → Settings → Connectors → Add custom MCP connector
+#    URL: the tunnel URL;  Token: $RUBIEN_MCP_BEARER
 ```
 
-Save the bearer token — you'll need it to reconnect after restarts.
+Save the token — you need it to reconnect after restarts.
+
+### Security model
 
-## Security model
+The remote path is **single-user personal use only.**
 
-This server is designed for **single-user personal use** only.
+- The bearer token is a long-lived static secret — no rotation, revocation, rate limiting, or replay protection. Treat it like an SSH key; regenerate if leaked.
+- Cloudflare Tunnel terminates TLS, so the token travels over HTTPS. A plaintext tunnel (e.g. raw ngrok HTTP) exposes it to sniffing.
+- A leaked URL without the token is safe (every request gets a 401) — but rotate both if in doubt.
 
-- The bearer token is a long-lived static secret. There's no rotation, revocation, rate limiting, or replay protection.
-- The server will happily accept any request with the correct token. Don't paste the token into anything you don't trust, and treat a leaked token like an SSH key — regenerate immediately.
-- Cloudflare Tunnel provides TLS termination; the token travels over HTTPS. If you use a plaintext tunnel (e.g. raw ngrok HTTP) the token can be sniffed.
-- A leaked URL without the token is safe — every request gets a 401 — but rotate both if in doubt.
+Multi-user would need a real auth story: OAuth, short-lived tokens, per-client revocation.
 
-If this setup ever becomes multi-user, the auth layer needs a real story: OAuth, short-lived tokens, and per-client revocation.
+## Optional configuration
+
+### Pin the library directory
+
+By default the CLI resolves its own library location. To force one, set `RUBIEN_LIBRARY_ROOT` to the directory containing `library.sqlite`:
+
+- Claude Code: `claude mcp add rubien --env RUBIEN_LIBRARY_ROOT=<dir> -- npx -y rubien-mcp-server`
+- Claude Desktop: add `"env": { "RUBIEN_LIBRARY_ROOT": "<dir>" }` beside `command`/`args`.
+
+| Host | Directory |
+|---|---|
+| Mac (sandboxed app) | `~/Library/Group Containers/9TXK4V3SS8.com.rubien.shared/Rubien` |
+| Mac (unsandboxed dev) | `~/Library/Application Support/Rubien` |
+| Linux | `~/.local/share/rubien` (or `$XDG_DATA_HOME/rubien`) |
+
+### How the server finds `rubien-cli`
+
+First hit wins:
+
+1. `$RUBIEN_CLI` (explicit path)
+2. `/Applications/Rubien.app/Contents/Helpers/rubien-cli` (Mac)
+3. `~/Applications/Rubien.app/Contents/Helpers/rubien-cli` (Mac)
+4. `./build/Rubien.app/Contents/Helpers/rubien-cli` (dev build, Mac)
+5. `rubien-cli` on `PATH` (Linux installs land here)
+
+**On Mac, prefer the bundled helper** (2–4): it's signed with the App Group entitlement and reads the same `library.sqlite` as the app. A bare `rubien-cli` on PATH is usually an unentitled dev build hitting a *different* database (see "Database location" in `Docs/CLI-Reference.md`).
+
+**On Linux**, everything works except `rubien_get_sync_status` (no CloudKit — the `sync` subcommand isn't built).
+
+### Run a local checkout
+
+For development, point the client at a built `dist/` (see [Development](#development)):
+
+```bash
+claude mcp add rubien -- node $(pwd)/dist/index.js        # Claude Code
+```
+```json
+{ "mcpServers": { "rubien": { "command": "node", "args": ["/abs/path/to/mcp-server/dist/index.js"] } } }
+```
 
 ## Tool catalog
 
-Roughly 36 tools covering every `rubien-cli` subcommand mode. Names are `rubien_<subject>_<action>` so Claude can pick the right tool from a single-word hint:
+27 tools on the `{op}_{target}` grid — CRUD operations always carry the target suffix (`create_reference`, `update_property`); a bare verb appears only when the operation is unique and unambiguous (`cite`, `export`):
 
 | Surface | Tools |
 |---|---|
-| References | `rubien_search`, `rubien_list`, `rubien_get`, `rubien_add`, `rubien_update`, `rubien_delete` |
-| Citations | `rubien_cite`, `rubien_styles_list` |
-| Import/Export | `rubien_import`, `rubien_export` |
-| PDFs | `rubien_pdf_info`, `rubien_pdf_text`, `rubien_pdf_page_image`, `rubien_pdf_download`, `rubien_annotations_list` |
-| Web clips | `rubien_web_get`, `rubien_web_annotations` |
-| Properties (incl. Tags) | `rubien_properties_list`, `rubien_properties_create`, `rubien_properties_delete`, `rubien_properties_rename`, `rubien_properties_show`, `rubien_properties_hide`, `rubien_properties_add_option`, `rubien_properties_rename_option`, `rubien_properties_delete_option`, `rubien_properties_set`, `rubien_properties_add_values`, `rubien_properties_remove_values`, `rubien_properties_clear` |
-| Saved views | `rubien_views_list`, `rubien_views_create`, `rubien_views_delete`, `rubien_views_rename`, `rubien_views_query` |
-| Sync | `rubien_sync_status` (Mac-only — errors on Linux hosts) |
+| References | `rubien_search_references`, `rubien_list_references`, `rubien_get_reference`, `rubien_create_reference`, `rubien_update_reference`, `rubien_delete_reference` |
+| Citations | `rubien_cite`, `rubien_list_styles` |
+| Export | `rubien_export` |
+| Reading | `rubien_read_text`, `rubien_read_annotations`, `rubien_grep_text` |
+| PDFs | `rubien_get_pdf_info`, `rubien_render_pdf_page`, `rubien_download_pdf` |
+| Properties (columns + options, incl. Tags) | `rubien_list_properties`, `rubien_create_property`, `rubien_update_property`, `rubien_delete_property`, `rubien_create_option`, `rubien_update_option`, `rubien_delete_option` |
+| Saved views | `rubien_list_views`, `rubien_create_view`, `rubien_update_view`, `rubien_delete_view` |
+| Sync | `rubien_get_sync_status` (Mac-only — errors on Linux) |
+
+`rubien_create_reference` is the **one door in**: pass exactly one of `source` (any locator — DOI / arXiv / PMID / PMCID / ISBN, paper URL, PDF/Markdown file URL, absolute file path, or folder path; the CLI routes it), `bibtex`, or `title`. It may return multiple items (multi-entry BibTeX, folders) and `status: "existing"` when dedup matched, in the unified `{items, summary, diagnostics}` envelope. Stdin (`"-"`) is intentionally unavailable through MCP.
 
-The PDF tools cover inspection and acquisition — `rubien_pdf_info` returns page count plus a flattened outline, `rubien_pdf_text` extracts text by page range or section title, `rubien_pdf_page_image` renders a page to PNG for figure inspection, and `rubien_pdf_download` fetches an open-access PDF for an existing reference and attaches it to the library. `rubien_annotations_list` returns the user's highlights/underlines/anchored-notes on the attached PDF.
+Per-reference property values (cells) are edited through `rubien_update_reference`'s `properties` payload — `{"Status": "Reading", "Tags": {"add": ["12"]}, "7": ["ml", "nlp"], "Themes": null}` — atomically alongside metadata fields. The option tools (`create_option` / `update_option` / `delete_option`) manage the *choices themselves* (including Tag rows for the built-in Tags property).
 
-The web-clip tools are the counterpart for clipped web pages — `rubien_web_get` returns the extracted body (markdown or HTML, paginated by character offset) along with `siteName` and `annotationCount`, and `rubien_web_annotations` returns highlights with a W3C TextQuoteSelector triple (`prefixText` / `anchorText` / `suffixText`) so the highlight can be located inside the body. Library-only — neither tool fetches from the network.
+Reading tools operate on any reference without your knowing whether it holds a PDF or a clipped web page. `rubien_read_text` returns the readable body text — the attached PDF or the clipped web page — routed automatically: omit `source` and `pages`/`sections` imply the PDF, `start` implies the web body, else PDF wins when both exist. Every response reports `source` (what was read) and `available` (which sources are readable now). PDF results are page-keyed (`pages[]` items with `text` + `sectionPath`, selected by a `pages` range or `sections` title-substrings); web results are one paginated body window (`content` + `contentLength`, `start`/`maxChars`; `contentFormat` markdown or HTML). `rubien_read_annotations` merges the user's highlights/underlines/anchored notes across both kinds into one array, each item tagged `source`; web items carry a W3C TextQuoteSelector triple (`prefixText`/`anchorText`/`suffixText`) that locates them inside the `rubien_read_text` body. `rubien_grep_text` is the lookup half of the same workflow: it finds *where* a reference's body mentions a phrase or regex — PDF hits grouped by page (`sectionPath` breadcrumbs), web hits as exact character offsets — so you can then pull just those spots with `rubien_read_text` (`pages` for PDF, `start` for web). All three are library-only — none hit the network.
 
-Destructive tools are tagged with `destructiveHint: true` so Claude Code's permission UI flags them. `rubien_delete` always passes `--force` — the confirmation happens in the MCP client permission UI, not in the CLI's TTY prompt. See the comment in `src/tools/references.ts` for rationale.
+PDF tools: `rubien_get_pdf_info` (page count, `hasTextLayer`, outline sections — call it before selecting `rubien_read_text` by `sections`), `rubien_render_pdf_page` (render a page to an image, for tables/figures/equations), `rubien_download_pdf` (fetch an open-access PDF and attach it to an existing reference).
+
+Destructive tools carry `destructiveHint: true` so Claude Code's permission UI flags them. `rubien_delete_reference` passes `--force`; confirmation happens in the client UI, not a CLI prompt (see `src/tools/references.ts`).
 
 ## Contract pinning
 
-Every tool's argument shape is defined in zod in the tool file; the expected *response* shape is in `src/schemas.ts`, mirroring the Swift DTOs in `Sources/RubienCLI/RubienCLI.swift` (search for `*DTO`). Crucial convention (see tests in `test/schemas.test.ts`):
+Argument shapes are zod schemas in each tool file; response shapes are in `src/schemas.ts`, mirroring the Swift `*DTO` types in `Sources/RubienCLI/RubienCLI.swift`. Convention (tested in `test/schemas.test.ts`):
 
-- `.optional()` in zod for Swift `Optional` fields — Swift's `JSONEncoder` **omits** nil optionals from output.
-- `.nullable()` only for `AlwaysEncodedOptional<T>` wrappers (currently just `DatabaseViewDTO.groupBy`).
+- `.optional()` for Swift `Optional` fields — `JSONEncoder` omits nil optionals.
+- `.nullable()` only for `AlwaysEncodedOptional<T>` (currently just `DatabaseViewDTO.groupBy`).
 
-If a Swift DTO changes, update both the Swift side and `src/schemas.ts` in the same commit, per the CLAUDE.md rule about keeping the CLI and data layer in lockstep.
+Change a Swift DTO → update `src/schemas.ts` in the same commit (CLAUDE.md CLI/data-layer lockstep rule).
 
 ## Development
 
-Build from a local checkout (instead of `npx`):
-
 ```bash
 cd mcp-server
 npm install
 npm run build         # → dist/
-npm test              # vitest unit tests
-```
-
-Watch mode:
-
-```bash
-npm run dev       # tsc --watch
-npm run test:watch
+npm test              # vitest
+npm run dev           # tsc --watch
 ```
 
-MCP Inspector is the fastest way to poke at tool schemas by hand:
+Poke at tool schemas by hand with MCP Inspector:
 
 ```bash
 npx @modelcontextprotocol/inspector node dist/index.js

package/dist/cli.js

@@ -52,9 +52,12 @@ export function resolveCliPath() {
  * Invoke rubien-cli with the given argv and return the parsed result.
  *
  * Contract: on exit 0, stdout is JSON (default) or plain text (`textMode`).
- * On non-zero exit, stderr is `{"error": "..."}` per the contract pinned in
- * Tests/RubienCLITests/SwiftLibCLITests.swift:189; this function throws a
- * CliError with that message.
+ * On non-zero exit, stderr carries a structured JSON error envelope — either
+ * plain `{"error": "..."}` or a richer shape like the `unresolved-selectors`
+ * envelope (`{"error", "ids", "names"}`) or the all-failed create-reference
+ * envelope (`{"items", "summary"}`). Per spec §4.6 the envelope must reach
+ * the agent VERBATIM — no field extraction — so CliError.message is the raw
+ * stderr text.
  */
 export async function invokeCli(args, options = {}) {
     const cliPath = resolveCliPath();
@@ -66,7 +69,7 @@ export async function invokeCli(args, options = {}) {
         });
         // Close stdin unconditionally. Even when we have nothing to pipe, leaving
         // it open causes subcommands that call `readDataToEndOfFile()` (like
-        // `import -`) to block until the timeout fires.
+        // `add --source -`) to block until the timeout fires.
         if (child.child.stdin) {
             if (options.stdin !== undefined) {
                 child.child.stdin.write(options.stdin);
@@ -86,20 +89,10 @@ export async function invokeCli(args, options = {}) {
         // execFile error shape: { code, signal, stdout, stderr, message }
         const e = err;
         const stderr = (e.stderr ?? "").trim();
-        let parsedError;
-        if (stderr.length > 0) {
-            try {
-                const parsed = JSON.parse(stderr);
-                if (parsed && typeof parsed === "object" && "error" in parsed) {
-                    parsedError = String(parsed.error);
-                }
-            }
-            catch {
-                // stderr wasn't JSON; fall through and use raw text.
-            }
-        }
-        const message = parsedError ??
-            (stderr.length > 0 ? stderr : (e.message ?? "rubien-cli invocation failed"));
+        // Raw pass-through (§4.6): structured envelopes (unresolved-selectors,
+        // all-failed create envelopes) must survive to the agent unmodified —
+        // extracting `.error` here would silently drop `ids`/`names`/`items`.
+        const message = stderr.length > 0 ? stderr : (e.message ?? "rubien-cli invocation failed");
         throw new CliError(message, typeof e.code === "number" ? e.code : null, stderr);
     }
 }

package/dist/cli.js.map

@@ -1 +1 @@
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package/dist/index.js

@@ -21,11 +21,11 @@ Options:
 
 Examples:
   # Claude Code
-  claude mcp add rubien node /path/to/mcp-server/dist/index.js
+  claude mcp add rubien -- npx -y rubien-mcp-server
 
-  # claude.ai (remote MCP)
+  # claude.ai (remote MCP) — same package, HTTP mode
   RUBIEN_MCP_BEARER=$(openssl rand -hex 32) \\
-    node dist/index.js --http --port 4000 --bearer-token "$RUBIEN_MCP_BEARER"
+    npx -y rubien-mcp-server --http --port 4000 --bearer-token "$RUBIEN_MCP_BEARER"
   # then: cloudflared tunnel --url http://localhost:4000
 `;
 function parseCliArgs(argv) {

package/dist/schemas.js

@@ -13,7 +13,7 @@ const isoDateString = z
     .string()
     .describe("ISO-8601 timestamp with millisecond precision, e.g. 2026-04-24T12:00:00.000Z");
 export const CustomPropertyValueDTO = z.object({
-    propertyId: z.string(),
+    propertyId: z.number().int(),
     name: z.string(),
     type: z.string(),
     value: z.string(),
@@ -60,7 +60,7 @@ export const PropertyOptionDTO = z.object({
     color: z.string(),
 });
 export const PropertyDefinitionDTO = z.object({
-    id: z.string(),
+    id: z.number().int(),
     name: z.string(),
     type: z.string(),
     options: z.array(PropertyOptionDTO),
@@ -69,25 +69,48 @@ export const PropertyDefinitionDTO = z.object({
     defaultFieldKey: z.string().optional(),
     isVisible: z.boolean(),
 });
-// PDF-download status DTO emitted by `add --identifier --download-pdf` and by
-// `pdf download <id>`. Mirrors PDFDownloadStatusDTO in RubienCLI.swift.
-// `action` is the raw value of PDFDownloadAction (downloaded | already-attached
-// | already-pending | skipped). All fields except `ok` use plain `Optional` in
-// Swift → key omitted when nil → `.optional()` here.
+// PDF-download status DTO emitted by the create-reference resolver route's
+// PDF fetch and by `pdf download <id>`. Mirrors PDFDownloadStatusDTO in
+// RubienCLI.swift. `action` is the raw value of PDFDownloadAction (downloaded
+// | replaced | already-attached | already-pending | skipped). All fields
+// except `ok` use plain `Optional` in Swift → key omitted when nil →
+// `.optional()` here.
 export const PDFDownloadStatusDTO = z.object({
     ok: z.boolean(),
     action: z.string().optional(),
     filename: z.string().optional(),
     error: z.string().optional(),
 });
-// Envelope returned by `add` (single object) or `add --bibtex` (array of these).
-// `status` mirrors AppDatabase.ReferenceSaveResult.
-// `pdfDownload` is an AlwaysEncodedOptional in Swift, so it's always present
-// in the JSON — explicit `null` when --download-pdf wasn't set.
-export const AddStatusOutput = z.object({
-    reference: ReferenceDTO,
-    status: z.enum(["created", "existing"]),
-    pdfDownload: PDFDownloadStatusDTO.nullable(),
+// Unified create-reference envelope (spec §5.4) — one shape for every route
+// (`add --source` / `--bibtex` / `--title`). Swift-Optional contract as
+// everywhere: absent keys, never null. `diagnostics` appears only when the
+// route produces it; `pdfDownload` only when a fetch was attempted.
+export const CreateReferenceItem = z.object({
+    reference: ReferenceDTO.optional(),
+    status: z.enum(["created", "existing", "queued", "failed"]),
+    intakeId: z.number().int().optional(),
+    input: z.string(),
+    pdfDownload: PDFDownloadStatusDTO.optional(),
+    error: z.string().optional(),
+});
+export const CreateReferenceEnvelope = z.object({
+    items: z.array(CreateReferenceItem),
+    summary: z.object({
+        created: z.number().int(),
+        existing: z.number().int(),
+        queued: z.number().int(),
+        failed: z.number().int(),
+    }),
+    diagnostics: z
+        .object({
+        file: z.string().optional(),
+        property: z.string().optional(),
+        value: z.string().optional(),
+        attached: z.number().int().optional(),
+        duplicatesSkipped: z.number().int().optional(),
+        missingPDFs: z.array(z.string()).optional(),
+    })
+        .optional(),
 });
 // TagDTO retired alongside the rubien_tags_* MCP tool family. Tag rows now
 // surface as inline options on the built-in Tags PropertyDefinition (see
@@ -130,13 +153,93 @@ export const DatabaseViewDTO = z.object({
     dateCreated: isoDateString,
     dateModified: isoDateString,
 });
-export const AnnotationDTO = z.object({
+// Unified read-tool output mirrors (RubienCLI `read text` / `read annotations`).
+// Superseded the permissive AnnotationDTO, which was retired alongside the
+// kind-specific rubien_web_* / rubien_annotations_list tools.
+export const ReadTextPdfOutput = z.object({
+    id: z.number().int(),
+    source: z.literal("pdf"),
+    available: z.array(z.enum(["pdf", "web"])),
+    pageCount: z.number().int(),
+    selection: z.object({
+        mode: z.string(),
+        pages: z.string().optional(),
+        requested: z.array(z.string()).optional(),
+        matchedSections: z.array(z.string()).optional(),
+        unmatched: z.array(z.string()).optional(),
+    }),
+    pages: z.array(z.object({
+        index: z.number().int(),
+        text: z.string(),
+        sectionPath: z.array(z.string()),
+    })),
+    truncated: z.boolean(),
+    hasTextLayer: z.boolean(),
+});
+export const ReadTextWebOutput = z.object({
+    id: z.number().int(),
+    source: z.literal("web"),
+    available: z.array(z.enum(["pdf", "web"])),
+    url: z.string().optional(),
+    siteName: z.string().optional(),
+    contentFormat: z.enum(["markdown", "html"]),
+    content: z.string(),
+    contentLength: z.number().int(),
+    start: z.number().int(),
+    returnedChars: z.number().int(),
+    truncated: z.boolean(),
+    annotationCount: z.number().int(),
+});
+export const ReadAnnotationItem = z.object({
+    source: z.enum(["pdf", "web"]),
     id: z.number().int(),
     type: z.string(),
-    color: z.string().optional(),
+    color: z.string(),
+    noteText: z.string().optional(),
+    dateCreated: isoDateString,
+    dateModified: isoDateString,
     pageIndex: z.number().int().optional(),
     selectedText: z.string().optional(),
-    noteText: z.string().optional(),
+    anchorText: z.string().optional(),
+    prefixText: z.string().optional(),
+    suffixText: z.string().optional(),
+});
+// Unified grep-tool output mirrors (RubienCLI `grep <id> <query>`). PDF hits are
+// page-grouped (PageSearchHit); web hits carry character offsets (GrepWebMatch).
+export const GrepTextPdfOutput = z.object({
+    id: z.number().int(),
+    source: z.literal("pdf"),
+    available: z.array(z.enum(["pdf", "web"])),
+    query: z.string(),
+    isRegex: z.boolean(),
+    pageCount: z.number().int(),
+    hasTextLayer: z.boolean(),
+    totalMatches: z.number().int(),
+    totalMatchingPages: z.number().int(),
+    truncated: z.boolean(),
+    pages: z.array(z.object({
+        page: z.number().int(),
+        sectionPath: z.array(z.string()),
+        matchCount: z.number().int(),
+        snippetsTruncated: z.boolean(),
+        snippets: z.array(z.string()),
+    })),
+});
+export const GrepTextWebOutput = z.object({
+    id: z.number().int(),
+    source: z.literal("web"),
+    available: z.array(z.enum(["pdf", "web"])),
+    query: z.string(),
+    isRegex: z.boolean(),
+    contentLength: z.number().int(),
+    totalMatches: z.number().int(),
+    totalEntries: z.number().int(),
+    truncated: z.boolean(),
+    matches: z.array(z.object({
+        start: z.number().int().nonnegative(),
+        matchCount: z.number().int(),
+        snippet: z.string(),
+    })),
 });
 export const StyleDTO = z.object({
     id: z.string(),
@@ -159,8 +262,8 @@ export const SyncStatusDTO = z
 })
     .passthrough(); // sync status is relatively fluid; keep forward-compat
 export const DeleteResultDTO = z.object({ deleted: z.string() });
-export const ImportResultDTO = z
-    .object({ imported: z.number().int(), file: z.string() })
-    .passthrough();
-export const CliErrorDTO = z.object({ error: z.string() });
+// (ImportResultDTO removed with the `import` subcommand; CliErrorDTO removed
+// with the verbatim-stderr change — errors are now raw envelope text, which
+// may be a structured `{error, ids, names}` / `{items, summary}` shape, not a
+// plain `{error}` object.)
 //# sourceMappingURL=schemas.js.map

package/dist/schemas.js.map

@@ -1 +1 @@
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