rubien-mcp-server 0.2.0 → 0.3.0

package/README.md

@@ -47,6 +47,17 @@ claude mcp add rubien -- npx -y rubien-mcp-server
 
 **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.
 
+### 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:
+
+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.
+
+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).
+
+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.
@@ -103,7 +114,7 @@ First hit wins:
 
 **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_sync_status` (no CloudKit — the `sync` subcommand isn't built).
+**On Linux**, everything works except `rubien_get_sync_status` (no CloudKit — the `sync` subcommand isn't built).
 
 ### Run a local checkout
 
@@ -118,26 +129,28 @@ claude mcp add rubien -- node $(pwd)/dist/index.js        # Claude Code
 
 ## Tool catalog
 
-35 tools, one per `rubien-cli` subcommand mode, named `rubien_<subject>_<action>`:
+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` |
+| 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_pdf_info`, `rubien_pdf_page_image`, `rubien_pdf_download` |
-| 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) |
+| 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.
 
-`rubien_import` accepts an absolute path on the host or a direct HTTP(S) URL with a `.pdf`, `.md`, or `.markdown` path extension. Direct URLs are validated by `rubien-cli` before import; stdin (`"-"`) is intentionally unavailable through MCP.
+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).
 
 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.
 
-PDF tools: `rubien_pdf_info` (page count, `hasTextLayer`, outline sections — call it before selecting `rubien_read_text` by `sections`), `rubien_pdf_page_image` (render a page to an image, for tables/figures/equations), `rubien_pdf_download` (fetch an open-access PDF and attach it).
+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` passes `--force`; confirmation happens in the client UI, not a CLI prompt (see `src/tools/references.ts`).
+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
 

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);
     }
 }

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+{"version":3,"file":"cli.js","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAC9C,OAAO,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AACrC,OAAO,EAAE,SAAS,EAAE,MAAM,WAAW,CAAC;AACtC,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAGjC,MAAM,aAAa,GAAG,SAAS,CAAC,QAAQ,CAAC,CAAC;AAE1C,MAAM,kBAAkB,GAAG,MAAM,CAAC;AAClC,MAAM,kBAAkB,GAAG,EAAE,GAAG,IAAI,GAAG,IAAI,CAAC;AAE5C,MAAM,OAAO,QAAS,SAAQ,KAAK;IAGf;IACA;IAHlB,YACE,OAAe,EACC,QAAuB,EACvB,MAAc;QAE9B,KAAK,CAAC,OAAO,CAAC,CAAC;QAHC,aAAQ,GAAR,QAAQ,CAAe;QACvB,WAAM,GAAN,MAAM,CAAQ;QAG9B,IAAI,CAAC,IAAI,GAAG,UAAU,CAAC;IACzB,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,UAAU,cAAc;IAC5B,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC;IAC3C,IAAI,WAAW,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC1C,oEAAoE;QACpE,gDAAgD;QAChD,IAAI,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CACb,oDAAoD,WAAW,EAAE,CAClE,CAAC;QACJ,CAAC;QACD,OAAO,WAAW,CAAC;IACrB,CAAC;IAED,MAAM,UAAU,GAAG;QACjB,sDAAsD;QACtD,IAAI,CAAC,OAAO,EAAE,EAAE,qDAAqD,CAAC;QACtE,kDAAkD;QAClD,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,8CAA8C,CAAC;QACnE,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,iDAAiD,CAAC;KACvE,CAAC;IACF,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;QAC3B,IAAI,UAAU,CAAC,CAAC,CAAC;YAAE,OAAO,CAAC,CAAC;IAC9B,CAAC;IAED,2EAA2E;IAC3E,sEAAsE;IACtE,gDAAgD;IAChD,OAAO,YAAY,CAAC;AACtB,CAAC;AAWD;;;;;;;;;;GAUG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAAc,EACd,UAAsB,EAAE;IAExB,MAAM,OAAO,GAAG,cAAc,EAAE,CAAC;IACjC,MAAM,OAAO,GAAG,OAAO,CAAC,SAAS,IAAI,kBAAkB,CAAC;IAExD,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,aAAa,CAAC,OAAO,EAAE,IAAI,EAAE;YACzC,OAAO;YACP,SAAS,EAAE,kBAAkB;SAC9B,CAAC,CAAC;QACH,0EAA0E;QAC1E,qEAAqE;QACrE,sDAAsD;QACtD,IAAI,KAAK,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC;YACtB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;gBAChC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;YACzC,CAAC;YACD,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;QAC1B,CAAC;QACD,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,KAAK,CAAC;QAE/B,IAAI,OAAO,CAAC,QAAQ,EAAE,CAAC;YACrB,OAAO,EAAE,MAAM,EAAE,aAAa,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;QACvD,CAAC;QAED,MAAM,OAAO,GAAG,MAAM,CAAC,IAAI,EAAE,CAAC;QAC9B,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,IAAI,CAAC;QACtC,OAAO,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IAC7B,CAAC;IAAC,OAAO,GAAY,EAAE,CAAC;QACtB,kEAAkE;QAClE,MAAM,CAAC,GAAG,GAMT,CAAC;QACF,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;QACvC,uEAAuE;QACvE,sEAAsE;QACtE,sEAAsE;QACtE,MAAM,OAAO,GACX,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,IAAI,8BAA8B,CAAC,CAAC;QAC7E,MAAM,IAAI,QAAQ,CAChB,OAAO,EACP,OAAO,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,EAC1C,MAAM,CACP,CAAC;IACJ,CAAC;AACH,CAAC;AAED,SAAS,aAAa,CAAC,IAAc;IACnC,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC;IACrC,IAAI,GAAG,IAAI,CAAC,IAAI,GAAG,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM;QAAE,OAAO,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC;IAC5D,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACpC,IAAI,QAAQ,IAAI,CAAC,IAAI,QAAQ,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM;QAAE,OAAO,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAC;IAC3E,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;iEACiE;AACjE,MAAM,CAAC,KAAK,UAAU,cAAc,CAAI,IAAc,EAAE,UAAsB,EAAE;IAC9E,OAAO,CAAC,MAAM,SAAS,CAAC,IAAI,EAAE,OAAO,CAAC,CAAM,CAAC;AAC/C,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,CAAC,SAAS,CAAC,EAAE,EAAE,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC;QAClE,IACE,MAAM;YACN,OAAO,MAAM,KAAK,QAAQ;YAC1B,OAAQ,MAAkC,CAAC,OAAO,KAAK,QAAQ;YAC/D,OAAQ,MAAkC,CAAC,KAAK,KAAK,QAAQ,EAC7D,CAAC;YACD,OAAO,MAA+B,CAAC;QACzC,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC"}

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
@@ -239,8 +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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package/dist/server.js

@@ -9,7 +9,7 @@ import { registerPdfTools } from "./tools/pdf.js";
 import { registerReadTools } from "./tools/read.js";
 export const SERVER_INFO = {
     name: "rubien-mcp-server",
-    version: "0.2.0",
+    version: "0.3.0",
 };
 export function buildServer() {
     const server = new McpServer(SERVER_INFO, {

package/dist/tools/citations.js

@@ -13,13 +13,13 @@ const CITE_FORMATS = ["text", "bibliography", "docx-cc"];
 export function registerCitationTools(server) {
     server.registerTool("rubien_cite", {
         title: "Format citations",
-        description: "Generate formatted citations for one or more references. Output shape varies by format: `text` → { style, inline, bibliography }, `bibliography` → { style, entries }, `docx-cc` → { tag, text, style, isShortTag?, fallbackPayload? }. Use arbitrary CSL style IDs from `rubien_styles_list` if needed.",
+        description: "Generate formatted citations for one or more references. Output shape varies by format: `text` → { style, inline, bibliography }, `bibliography` → { style, entries }, `docx-cc` → { tag, text, style, isShortTag?, fallbackPayload? }. Use arbitrary CSL style IDs from `rubien_list_styles` if needed.",
         inputSchema: {
             ids: z.array(z.number().int()).min(1).describe("Reference IDs to cite"),
             style: z
                 .string()
                 .optional()
-                .describe(`Citation style (default apa). Built-ins: ${BUILTIN_STYLES.join(", ")}. Any CSL ID from rubien_styles_list also works.`),
+                .describe(`Citation style (default apa). Built-ins: ${BUILTIN_STYLES.join(", ")}. Any CSL ID from rubien_list_styles also works.`),
             format: z
                 .enum(CITE_FORMATS)
                 .optional()
@@ -34,7 +34,7 @@ export function registerCitationTools(server) {
             args.push("--format", format);
         return runCliAsTool(args);
     });
-    server.registerTool("rubien_styles_list", {
+    server.registerTool("rubien_list_styles", {
         title: "List citation styles",
         description: "List all available citation styles (built-in + installed CSL). Use the returned `id` as the `style` argument to rubien_cite.",
         inputSchema: {},

package/dist/tools/io.js

@@ -1,36 +1,8 @@
 import { z } from "zod";
-import { flagsFromOptions, runCliAsTool } from "../toolHelpers.js";
+import { runCliAsTool } from "../toolHelpers.js";
+// `rubien_import` was folded into `rubien_create_reference` (references.ts) in
+// the 0.3.0 catalog — one door for every input; the CLI routes the locator.
 export function registerIOTools(server) {
-    server.registerTool("rubien_import", {
-        title: "Import a PDF, BibTeX/RIS, Markdown, or folder",
-        description: "Import references from a local file (PDF .pdf / BibTeX .bib / RIS .ris / Markdown .md — Obsidian Web Clipper frontmatter is mapped, plain notes import too), a direct HTTP(S) PDF/Markdown file URL with a supported path extension, or a folder (Zotero export, or a folder of .md files). Folder imports stamp a single-/multi-select property value on every imported reference via property + value (default: Tags = folder basename). A folder containing both .bib and .md needs format to disambiguate.",
-        inputSchema: {
-            file: z
-                .string()
-                .describe("Absolute path on the host, or a direct HTTP(S) URL with a .pdf, .md, or .markdown path extension. Stdin piping ('-') is not supported through the MCP wrapper; if you need it, invoke rubien-cli directly."),
-            format: z
-                .enum(["bib", "ris", "md"])
-                .optional()
-                .describe("For folders, disambiguates when both .bib and .md are present. Direct HTTP(S) URLs must have a .pdf, .md, or .markdown path extension."),
-            property: z
-                .string()
-                .optional()
-                .describe("(Folder imports) Property name to stamp on imported refs"),
-            value: z
-                .string()
-                .optional()
-                .describe("(Folder imports) Value for --property on imported refs"),
-        },
-        annotations: { destructiveHint: true },
-    }, async ({ file, format, property, value }) => runCliAsTool([
-        "import",
-        file,
-        ...flagsFromOptions({
-            "--format": format,
-            "--property": property,
-            "--value": value,
-        }),
-    ], { timeoutMs: 180_000 }));
     server.registerTool("rubien_export", {
         title: "Export references",
         description: "Export the library (or a subset) as JSON, BibTeX, or RIS. BibTeX/RIS output is plain text; JSON is a ReferenceDTO[] array.",

package/dist/tools/io.js.map

@@ -1 +1 @@
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+{"version":3,"file":"io.js","sourceRoot":"","sources":["../../src/tools/io.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAEjD,+EAA+E;AAC/E,4EAA4E;AAE5E,MAAM,UAAU,eAAe,CAAC,MAAiB;IAC/C,MAAM,CAAC,YAAY,CACjB,eAAe,EACf;QACE,KAAK,EAAE,mBAAmB;QAC1B,WAAW,EACT,4HAA4H;QAC9H,WAAW,EAAE;YACX,MAAM,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC,QAAQ,EAAE;iBACjD,QAAQ,CAAC,iBAAiB,CAAC;SAC/B;QACD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE;KACpC,EACD,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;QACnB,MAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,CAAC;QACxB,IAAI,MAAM;YAAE,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC;QAC1C,MAAM,QAAQ,GAAG,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,KAAK,CAAC;QACzD,OAAO,YAAY,CAAC,IAAI,EAAE,EAAE,QAAQ,EAAE,CAAC,CAAC;IAC1C,CAAC,CACF,CAAC;AACJ,CAAC"}

package/dist/tools/pdf.js

@@ -2,7 +2,7 @@ import { z } from "zod";
 import { CliError, invokeCliTyped } from "../cli.js";
 import { flagsFromOptions, runCliAsTool } from "../toolHelpers.js";
 export function registerPdfTools(server) {
-    server.registerTool("rubien_pdf_info", {
+    server.registerTool("rubien_get_pdf_info", {
         title: "Probe PDF metadata + outline",
         description: "Return page count, hasTextLayer (sampled across first/middle/last page), file size, isEncrypted, documentTitle, and the flattened outline `sections` (or null when the PDF has no outline). Each section carries title, level (1=top), startPage, and endPage; parent ranges span their descendants. Call this before `rubien_read_text` when you plan to select by `sections` or page ranges.",
         inputSchema: {
@@ -10,7 +10,7 @@ export function registerPdfTools(server) {
         },
         annotations: { readOnlyHint: true },
     }, async ({ id }) => runCliAsTool(["pdf", "info", String(id)]));
-    server.registerTool("rubien_pdf_page_image", {
+    server.registerTool("rubien_render_pdf_page", {
         title: "Render a PDF page as an image",
         description: "Render a single PDF page (1-indexed) and return it as an MCP image content block. Use this when text extraction is empty/garbled (scanned page, dense math) or when a figure/table is referenced in the surrounding text. Defaults: JPEG at scale=2.0 (~192 DPI) with quality stepdown to honor maxBytes. PNG mode is opt-in for lossless output but hard-fails on maxBytes.",
         inputSchema: {
@@ -78,9 +78,9 @@ export function registerPdfTools(server) {
             throw err;
         }
     });
-    server.registerTool("rubien_pdf_download", {
-        title: "Download the open-access PDF for a reference",
-        description: "Fetch the open-access PDF (via DOI or arXiv resolution) and attach it to the reference. Skip-if-attached by default; pass `force: true` to detach the existing PDF and re-download. Side effects: writes a file under the library's PDF storage and inserts a pdfCache row + pdfUploadQueue row (so the running app's sync engine will push to CloudKit). Returns `{ id, ok, action, filename? }` where `action` is `\"downloaded\" | \"replaced\" | \"already-attached\" | \"already-pending\"`. Errors (isError) when the reference is missing, has no DOI/arXiv, or the network fetch fails. Long-running — up to 5 minutes.",
+    server.registerTool("rubien_download_pdf", {
+        title: "Download the open-access PDF for an existing reference",
+        description: "Fetch the open-access PDF (via DOI or arXiv resolution) and attach it to an EXISTING reference (creation via rubien_create_reference fetches PDFs itself with `downloadPdf`). Skip-if-attached by default; pass `force: true` to detach the existing PDF and re-download. Side effects: writes a file under the library's PDF storage and inserts a pdfCache row + pdfUploadQueue row (so the running app's sync engine will push to CloudKit). Returns `{ id, ok, action, filename? }` where `action` is `\"downloaded\" | \"replaced\" | \"already-attached\" | \"already-pending\"`. Errors (isError) when the reference is missing, has no DOI/arXiv, or the network fetch fails. Long-running — up to 5 minutes.",
         inputSchema: {
             id: z.number().int().describe("Reference ID"),
             force: z

package/dist/tools/pdf.js.map

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