diff --git a/README.md b/README.md
index 4ed52213..746513ac 100644
--- a/README.md
+++ b/README.md
@@ -327,7 +327,7 @@ pip install paper-search-mcp
   "mcpServers": {
     "paper-search-mcp": {
       "command": "python",
-      "args": ["-m", "paper_search_mcp.server"],
+      "args": ["-m", "paper_search_mcp.mcp"],
       "env": {
         "PAPER_SEARCH_MCP_UNPAYWALL_EMAIL": "your@email.com",
         "PAPER_SEARCH_MCP_CORE_API_KEY": "",
@@ -419,7 +419,7 @@ git clone https://github.com/openags/paper-search-mcp.git
 cd paper-search-mcp
 
 # 3. Verify it runs (uv auto-resolves dependencies, no manual install needed)
-uv run -m paper_search_mcp.server
+uv run -m paper_search_mcp.mcp
 ```
 
 **Claude Desktop config** (replace the directory path with your actual clone location):
@@ -432,7 +432,7 @@ uv run -m paper_search_mcp.server
       "args": [
         "run",
         "--directory", "/path/to/paper-search-mcp",
-        "-m", "paper_search_mcp.server"
+        "-m", "paper_search_mcp.mcp"
       ],
       "env": {
         "PAPER_SEARCH_MCP_UNPAYWALL_EMAIL": "your@email.com",
@@ -451,7 +451,7 @@ uv run -m paper_search_mcp.server
 For example, if you cloned to `/Users/mac/Pengsong/paper-search-mcp`:
 
 ```json
-"args": ["run", "--directory", "/Users/mac/Pengsong/paper-search-mcp", "-m", "paper_search_mcp.server"]
+"args": ["run", "--directory", "/Users/mac/Pengsong/paper-search-mcp", "-m", "paper_search_mcp.mcp"]
 ```
 
 > `uv run` automatically installs dependencies into an isolated environment on first run — no `pip install` or `venv` needed.
diff --git a/claude-code/SKILL.md b/claude-code/SKILL.md
index 581bcdad..7fc49bd0 100644
--- a/claude-code/SKILL.md
+++ b/claude-code/SKILL.md
@@ -41,6 +41,24 @@ uv run --directory <REPO_PATH> paper-search read <source> <paper_id> [-o ./downl
 uv run --directory <REPO_PATH> paper-search sources
 ```
 
+### Tool
+
+The `tool` subcommand exposes API functions. Use it when you need source-specific functions or parameters that the regular top-level CLI does not expose. Positional API arguments stay positional, and optional arguments become kebab-case flags.
+
+```bash
+# List all shared API functions exposed through the tool subcommand
+uv run --directory <REPO_PATH> paper-search tool -h
+
+# Inspect the arguments for one specific shared API function
+uv run --directory <REPO_PATH> paper-search tool search_crossref -h
+
+# Crossref-specific filters and sorting
+uv run --directory <REPO_PATH> paper-search tool search_crossref "transformer attention" --filter from-pub-date:2024-01-01,has-full-text:true --sort published --order desc --max-results 2
+
+# Direct DOI lookup
+uv run --directory <REPO_PATH> paper-search tool get_crossref_paper_by_doi 10.1038/nature12373
+```
+
 ## Output
 
 `search` and `download` return JSON. `read` returns plain text. Config warnings go to stderr and can be ignored.
diff --git a/paper_search_mcp/server.py b/paper_search_mcp/api.py
similarity index 96%
rename from paper_search_mcp/server.py
rename to paper_search_mcp/api.py
index 194470e6..2b7189ea 100644
--- a/paper_search_mcp/server.py
+++ b/paper_search_mcp/api.py
@@ -1,11 +1,10 @@
-# paper_search_mcp/server.py
+# paper_search_mcp/api.py
 from typing import List, Dict, Optional, Any
 import asyncio
 import os
 import logging
 import re
 import httpx
-from mcp.server.fastmcp import FastMCP
 from .config import get_env
 from .academic_platforms.arxiv import ArxivSearcher
 from .academic_platforms.pubmed import PubMedSearcher
@@ -34,8 +33,6 @@
 # from .academic_platforms.hub import SciHubSearcher
 from .paper import Paper
 
-# Initialize MCP server
-mcp = FastMCP("paper_search_server")
 logger = logging.getLogger(__name__)
 
 # Instances of searchers
@@ -239,7 +236,6 @@ async def _try_repository_fallback(doi: str, title: str, save_path: str) -> tupl
     return None, "; ".join(repository_errors)
 
 
-@mcp.tool()
 async def search_papers(
     query: str,
     max_results_per_source: int = 5,
@@ -355,7 +351,6 @@ async def search_papers(
 
 
 # Tool definitions
-@mcp.tool()
 async def search_arxiv(query: str, max_results: int = 10, sort_by: str = 'relevance', sort_order: str = 'descending') -> List[Dict]:
     """Search academic papers from arXiv.
 
@@ -371,7 +366,6 @@ async def search_arxiv(query: str, max_results: int = 10, sort_by: str = 'releva
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_pubmed(query: str, max_results: int = 10, sort: str = 'relevance') -> List[Dict]:
     """Search academic papers from PubMed.
 
@@ -386,7 +380,6 @@ async def search_pubmed(query: str, max_results: int = 10, sort: str = 'relevanc
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_biorxiv(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from bioRxiv.
 
@@ -404,7 +397,6 @@ async def search_biorxiv(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_medrxiv(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from medRxiv.
 
@@ -422,7 +414,6 @@ async def search_medrxiv(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_google_scholar(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from Google Scholar.
 
@@ -436,7 +427,6 @@ async def search_google_scholar(query: str, max_results: int = 10) -> List[Dict]
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_iacr(
     query: str, max_results: int = 10, fetch_details: bool = True
 ) -> List[Dict]:
@@ -453,7 +443,6 @@ async def search_iacr(
     return [paper.to_dict() for paper in papers] if papers else []
 
 
-@mcp.tool()
 async def download_arxiv(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF of an arXiv paper.
 
@@ -466,7 +455,6 @@ async def download_arxiv(paper_id: str, save_path: str = "./downloads") -> str:
     return await asyncio.to_thread(arxiv_searcher.download_pdf, paper_id, save_path)
 
 
-@mcp.tool()
 async def download_pubmed(paper_id: str, save_path: str = "./downloads") -> str:
     """Attempt to download PDF of a PubMed paper.
 
@@ -482,7 +470,6 @@ async def download_pubmed(paper_id: str, save_path: str = "./downloads") -> str:
         return str(e)
 
 
-@mcp.tool()
 async def download_biorxiv(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF of a bioRxiv paper.
 
@@ -495,7 +482,6 @@ async def download_biorxiv(paper_id: str, save_path: str = "./downloads") -> str
     return biorxiv_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_medrxiv(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF of a medRxiv paper.
 
@@ -508,7 +494,6 @@ async def download_medrxiv(paper_id: str, save_path: str = "./downloads") -> str
     return medrxiv_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_iacr(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF of an IACR ePrint paper.
 
@@ -521,7 +506,6 @@ async def download_iacr(paper_id: str, save_path: str = "./downloads") -> str:
     return iacr_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_arxiv_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from an arXiv paper PDF.
 
@@ -538,7 +522,6 @@ async def read_arxiv_paper(paper_id: str, save_path: str = "./downloads") -> str
         return ""
 
 
-@mcp.tool()
 async def read_pubmed_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a PubMed paper.
 
@@ -551,7 +534,6 @@ async def read_pubmed_paper(paper_id: str, save_path: str = "./downloads") -> st
     return pubmed_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_biorxiv_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a bioRxiv paper PDF.
 
@@ -568,7 +550,6 @@ async def read_biorxiv_paper(paper_id: str, save_path: str = "./downloads") -> s
         return ""
 
 
-@mcp.tool()
 async def read_medrxiv_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a medRxiv paper PDF.
 
@@ -585,7 +566,6 @@ async def read_medrxiv_paper(paper_id: str, save_path: str = "./downloads") -> s
         return ""
 
 
-@mcp.tool()
 async def read_iacr_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from an IACR ePrint paper PDF.
 
@@ -602,7 +582,6 @@ async def read_iacr_paper(paper_id: str, save_path: str = "./downloads") -> str:
         return ""
 
 
-@mcp.tool()
 async def search_semantic(query: str, year: Optional[str] = None, max_results: int = 10) -> List[Dict]:
     """Search academic papers from Semantic Scholar.
 
@@ -620,7 +599,6 @@ async def search_semantic(query: str, year: Optional[str] = None, max_results: i
     return papers if papers else []
 
 
-@mcp.tool()
 async def download_semantic(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF of a Semantic Scholar paper.    
 
@@ -641,7 +619,6 @@ async def download_semantic(paper_id: str, save_path: str = "./downloads") -> st
     return semantic_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_semantic_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a Semantic Scholar paper. 
 
@@ -666,7 +643,6 @@ async def read_semantic_paper(paper_id: str, save_path: str = "./downloads") ->
         return ""
 
 
-@mcp.tool()
 async def search_crossref(
     query: str,
     max_results: int = 10,
@@ -695,7 +671,6 @@ async def search_crossref(
     return papers if papers else []
 
 
-@mcp.tool()
 async def get_crossref_paper_by_doi(doi: str) -> Dict:
     """Get a specific paper from CrossRef by its DOI.
 
@@ -711,7 +686,6 @@ async def get_crossref_paper_by_doi(doi: str) -> Dict:
     return paper.to_dict() if paper else {}
 
 
-@mcp.tool()
 async def download_crossref(paper_id: str, save_path: str = "./downloads") -> str:
     """Attempt to download PDF of a CrossRef paper.
 
@@ -731,7 +705,6 @@ async def download_crossref(paper_id: str, save_path: str = "./downloads") -> st
         return str(e)
 
 
-@mcp.tool()
 async def download_scihub(
     identifier: str,
     save_path: str = "./downloads",
@@ -753,7 +726,6 @@ async def download_scihub(
     return "Sci-Hub download failed. Try DOI first, then title, or change mirror URL."
 
 
-@mcp.tool()
 async def download_with_fallback(
     source: str,
     paper_id: str,
@@ -846,7 +818,6 @@ async def download_with_fallback(
     return "Download failed after OA fallback chain and Sci-Hub fallback. Details: " + " | ".join(attempt_errors)
 
 
-@mcp.tool()
 async def read_crossref_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Attempt to read and extract text content from a CrossRef paper.
 
@@ -863,7 +834,6 @@ async def read_crossref_paper(paper_id: str, save_path: str = "./downloads") ->
     return crossref_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def search_openalex(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from OpenAlex.
 
@@ -877,7 +847,6 @@ async def search_openalex(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_pmc(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from PubMed Central (PMC).
 
@@ -891,7 +860,6 @@ async def search_pmc(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_core(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from CORE.
 
@@ -905,7 +873,6 @@ async def search_core(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_europepmc(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from Europe PMC.
 
@@ -919,7 +886,6 @@ async def search_europepmc(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_dblp(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from dblp computer science bibliography.
 
@@ -933,7 +899,6 @@ async def search_dblp(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_openaire(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from OpenAIRE European Open Access infrastructure.
 
@@ -947,7 +912,6 @@ async def search_openaire(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_citeseerx(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from CiteSeerX digital library.
 
@@ -961,7 +925,6 @@ async def search_citeseerx(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_doaj(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from DOAJ (Directory of Open Access Journals).
 
@@ -975,7 +938,6 @@ async def search_doaj(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_base(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from BASE (Bielefeld Academic Search Engine).
 
@@ -989,7 +951,6 @@ async def search_base(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_zenodo(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from Zenodo open repository.
 
@@ -1003,7 +964,6 @@ async def search_zenodo(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_hal(query: str, max_results: int = 10) -> List[Dict]:
     """Search academic papers from HAL open archive.
 
@@ -1017,7 +977,6 @@ async def search_hal(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_ssrn(query: str, max_results: int = 10) -> List[Dict]:
     """Search metadata records from SSRN.
 
@@ -1033,7 +992,6 @@ async def search_ssrn(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def search_unpaywall(query: str, max_results: int = 10) -> List[Dict]:
     """Lookup a DOI via Unpaywall and return OA metadata.
 
@@ -1050,7 +1008,6 @@ async def search_unpaywall(query: str, max_results: int = 10) -> List[Dict]:
     return papers if papers else []
 
 
-@mcp.tool()
 async def read_dblp_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Attempt to read and extract text content from a dblp paper.
 
@@ -1066,7 +1023,6 @@ async def read_dblp_paper(paper_id: str, save_path: str = "./downloads") -> str:
     return dblp_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_dblp(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from dblp.
 
@@ -1082,7 +1038,6 @@ async def download_dblp(paper_id: str, save_path: str = "./downloads") -> str:
     return dblp_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_openaire_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Attempt to read and extract text content from an OpenAIRE paper.
 
@@ -1095,7 +1050,6 @@ async def read_openaire_paper(paper_id: str, save_path: str = "./downloads") ->
     return openaire_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_openaire(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from OpenAIRE.
 
@@ -1108,7 +1062,6 @@ async def download_openaire(paper_id: str, save_path: str = "./downloads") -> st
     return openaire_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_citeseerx_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a CiteSeerX paper.
 
@@ -1121,7 +1074,6 @@ async def read_citeseerx_paper(paper_id: str, save_path: str = "./downloads") ->
     return citeseerx_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_citeseerx(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from CiteSeerX.
 
@@ -1134,7 +1086,6 @@ async def download_citeseerx(paper_id: str, save_path: str = "./downloads") -> s
     return citeseerx_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_doaj_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a DOAJ paper.
 
@@ -1147,7 +1098,6 @@ async def read_doaj_paper(paper_id: str, save_path: str = "./downloads") -> str:
     return doaj_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_doaj(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from DOAJ.
 
@@ -1160,7 +1110,6 @@ async def download_doaj(paper_id: str, save_path: str = "./downloads") -> str:
     return doaj_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_base_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a BASE paper.
 
@@ -1173,7 +1122,6 @@ async def read_base_paper(paper_id: str, save_path: str = "./downloads") -> str:
     return base_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_base(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from BASE.
 
@@ -1186,7 +1134,6 @@ async def download_base(paper_id: str, save_path: str = "./downloads") -> str:
     return base_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_zenodo_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a Zenodo paper.
 
@@ -1199,7 +1146,6 @@ async def read_zenodo_paper(paper_id: str, save_path: str = "./downloads") -> st
     return zenodo_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_zenodo(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from Zenodo.
 
@@ -1212,7 +1158,6 @@ async def download_zenodo(paper_id: str, save_path: str = "./downloads") -> str:
     return zenodo_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_hal_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read and extract text content from a HAL paper.
 
@@ -1225,7 +1170,6 @@ async def read_hal_paper(paper_id: str, save_path: str = "./downloads") -> str:
     return hal_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_hal(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from HAL.
 
@@ -1238,7 +1182,6 @@ async def download_hal(paper_id: str, save_path: str = "./downloads") -> str:
     return hal_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_ssrn_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Read paper content from SSRN.
 
@@ -1253,7 +1196,6 @@ async def read_ssrn_paper(paper_id: str, save_path: str = "./downloads") -> str:
     return ssrn_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_ssrn(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from SSRN.
 
@@ -1268,7 +1210,6 @@ async def download_ssrn(paper_id: str, save_path: str = "./downloads") -> str:
     return ssrn_searcher.download_pdf(paper_id, save_path)
 
 
-@mcp.tool()
 async def read_openalex_paper(paper_id: str, save_path: str = "./downloads") -> str:
     """Attempt to read and extract text content from an OpenAlex paper.
 
@@ -1281,7 +1222,6 @@ async def read_openalex_paper(paper_id: str, save_path: str = "./downloads") ->
     return openalex_searcher.read_paper(paper_id, save_path)
 
 
-@mcp.tool()
 async def download_openalex(paper_id: str, save_path: str = "./downloads") -> str:
     """Download PDF for a paper from OpenAlex.
 
@@ -1298,7 +1238,6 @@ async def download_openalex(paper_id: str, save_path: str = "./downloads") -> st
 # Optional IEEE Xplore tools — registered only when API key is set
 # ---------------------------------------------------------------------------
 if ieee_searcher is not None:
-    @mcp.tool()
     async def search_ieee(query: str, max_results: int = 10) -> List[Dict]:
         """Search IEEE Xplore for papers.  Requires PAPER_SEARCH_MCP_IEEE_API_KEY (or IEEE_API_KEY).
 
@@ -1310,7 +1249,6 @@ async def search_ieee(query: str, max_results: int = 10) -> List[Dict]:
         """
         return await async_search(ieee_searcher, query, max_results)
 
-    @mcp.tool()
     async def download_ieee(paper_id: str, save_path: str = "./downloads") -> str:
         """Download a PDF from IEEE Xplore.  Requires PAPER_SEARCH_MCP_IEEE_API_KEY (or IEEE_API_KEY) and institutional access.
 
@@ -1322,7 +1260,6 @@ async def download_ieee(paper_id: str, save_path: str = "./downloads") -> str:
         """
         return await asyncio.to_thread(ieee_searcher.download_pdf, paper_id, save_path)
 
-    @mcp.tool()
     async def read_ieee_paper(paper_id: str, save_path: str = "./downloads") -> str:
         """Download and read an IEEE Xplore paper.  Requires PAPER_SEARCH_MCP_IEEE_API_KEY (or IEEE_API_KEY).
 
@@ -1339,7 +1276,6 @@ async def read_ieee_paper(paper_id: str, save_path: str = "./downloads") -> str:
 # Optional ACM Digital Library tools — registered only when API key is set
 # ---------------------------------------------------------------------------
 if acm_searcher is not None:
-    @mcp.tool()
     async def search_acm(query: str, max_results: int = 10) -> List[Dict]:
         """Search ACM Digital Library for papers.  Requires PAPER_SEARCH_MCP_ACM_API_KEY (or ACM_API_KEY).
 
@@ -1351,7 +1287,6 @@ async def search_acm(query: str, max_results: int = 10) -> List[Dict]:
         """
         return await async_search(acm_searcher, query, max_results)
 
-    @mcp.tool()
     async def download_acm(paper_id: str, save_path: str = "./downloads") -> str:
         """Download a PDF from ACM Digital Library.  Requires PAPER_SEARCH_MCP_ACM_API_KEY (or ACM_API_KEY) and institutional access.
 
@@ -1363,7 +1298,6 @@ async def download_acm(paper_id: str, save_path: str = "./downloads") -> str:
         """
         return await asyncio.to_thread(acm_searcher.download_pdf, paper_id, save_path)
 
-    @mcp.tool()
     async def read_acm_paper(paper_id: str, save_path: str = "./downloads") -> str:
         """Download and read an ACM Digital Library paper.  Requires PAPER_SEARCH_MCP_ACM_API_KEY (or ACM_API_KEY).
 
@@ -1376,9 +1310,74 @@ async def read_acm_paper(paper_id: str, save_path: str = "./downloads") -> str:
         return acm_searcher.read_paper(paper_id, save_path)
 
 
-def main():
-    mcp.run(transport="stdio")
+async def sources() -> Dict[str, List[str]]:
+    """List available paper sources for this installation."""
+    return {"sources": ALL_SOURCES}
+
+
+TOOLS = [
+    search_papers,
+    search_arxiv,
+    search_pubmed,
+    search_biorxiv,
+    search_medrxiv,
+    search_google_scholar,
+    search_iacr,
+    search_semantic,
+    search_crossref,
+    get_crossref_paper_by_doi,
+    search_openalex,
+    search_pmc,
+    search_core,
+    search_europepmc,
+    search_dblp,
+    search_openaire,
+    search_citeseerx,
+    search_doaj,
+    search_base,
+    search_zenodo,
+    search_hal,
+    search_ssrn,
+    search_unpaywall,
+    download_arxiv,
+    download_pubmed,
+    download_biorxiv,
+    download_medrxiv,
+    download_iacr,
+    download_semantic,
+    download_crossref,
+    download_scihub,
+    download_with_fallback,
+    download_dblp,
+    download_openaire,
+    download_citeseerx,
+    download_doaj,
+    download_base,
+    download_zenodo,
+    download_hal,
+    download_ssrn,
+    download_openalex,
+    read_arxiv_paper,
+    read_pubmed_paper,
+    read_biorxiv_paper,
+    read_medrxiv_paper,
+    read_iacr_paper,
+    read_semantic_paper,
+    read_crossref_paper,
+    read_dblp_paper,
+    read_openaire_paper,
+    read_citeseerx_paper,
+    read_doaj_paper,
+    read_base_paper,
+    read_zenodo_paper,
+    read_hal_paper,
+    read_ssrn_paper,
+    read_openalex_paper,
+    sources,
+]
 
+if ieee_searcher is not None:
+    TOOLS.extend([search_ieee, download_ieee, read_ieee_paper])
 
-if __name__ == "__main__":
-    main()
+if acm_searcher is not None:
+    TOOLS.extend([search_acm, download_acm, read_acm_paper])
diff --git a/paper_search_mcp/cli.py b/paper_search_mcp/cli.py
index 6edc6eb5..83dee855 100644
--- a/paper_search_mcp/cli.py
+++ b/paper_search_mcp/cli.py
@@ -10,6 +10,7 @@
 from typing import Any, Dict, List
 
 from .config import get_env
+from .tool_cli import add_tool_commands, cmd_tool
 from .academic_platforms.arxiv import ArxivSearcher
 from .academic_platforms.pubmed import PubMedSearcher
 from .academic_platforms.biorxiv import BioRxivSearcher
@@ -256,6 +257,10 @@ def build_parser() -> argparse.ArgumentParser:
     # sources
     sub.add_parser("sources", help="List available sources")
 
+    # tool
+    tool_parser = sub.add_parser("tool", help="Run a shared API command")
+    add_tool_commands(tool_parser)
+
     return parser
 
 
@@ -268,6 +273,7 @@ def main() -> None:
         "download": cmd_download,
         "read": cmd_read,
         "sources": cmd_sources,
+        "tool": cmd_tool,
     }
 
     exit_code = asyncio.run(dispatch[args.command](args))
diff --git a/paper_search_mcp/mcp.py b/paper_search_mcp/mcp.py
new file mode 100644
index 00000000..bad3944e
--- /dev/null
+++ b/paper_search_mcp/mcp.py
@@ -0,0 +1,20 @@
+"""MCP bootstrap for the shared paper search API."""
+
+from mcp.server.fastmcp import FastMCP
+
+from .api import TOOLS
+
+
+mcp = FastMCP("paper_search_server")
+
+for tool in TOOLS:
+    mcp.tool()(tool)
+
+
+def main() -> None:
+    """Run the MCP server over stdio."""
+    mcp.run(transport="stdio")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/paper_search_mcp/tool_cli.py b/paper_search_mcp/tool_cli.py
new file mode 100644
index 00000000..fdf6f623
--- /dev/null
+++ b/paper_search_mcp/tool_cli.py
@@ -0,0 +1,69 @@
+from __future__ import annotations
+
+import argparse
+import inspect
+import json
+from typing import Any, get_args, get_origin
+
+from .api import TOOLS
+
+
+def _argument_type(annotation: Any) -> Any:
+    if annotation is inspect._empty:
+        return str
+    origin = get_origin(annotation)
+    if origin is None:
+        return bool if annotation is bool else annotation
+    args = [arg for arg in get_args(annotation) if arg is not type(None)]
+    if len(args) == 1 and args[0] in (str, int, float, bool):
+        return args[0]
+    return str
+
+
+def _add_tool_argument(parser: argparse.ArgumentParser, name: str, parameter: inspect.Parameter) -> None:
+    arg_type = _argument_type(parameter.annotation)
+    if parameter.default is inspect._empty:
+        parser.add_argument(name, type=arg_type)
+        return
+    option = f"--{name.replace('_', '-')}"
+    if arg_type is bool:
+        action = "store_false" if parameter.default else "store_true"
+        parser.add_argument(option, action=action, default=parameter.default)
+        return
+    parser.add_argument(option, type=arg_type, default=parameter.default)
+
+
+def _add_tool_command(subparsers: Any, func: Any) -> None:
+    doc = inspect.getdoc(func) or ""
+    parser = subparsers.add_parser(
+        func.__name__,
+        help=doc.splitlines()[0] if doc else func.__name__,
+        description=doc,
+    )
+    for name, parameter in inspect.signature(func).parameters.items():
+        _add_tool_argument(parser, name, parameter)
+    parser.set_defaults(tool_handler=func)
+
+
+def add_tool_commands(tool_parser: argparse.ArgumentParser) -> None:
+    tool_subparsers = tool_parser.add_subparsers(dest="tool_name", required=True)
+    for tool in TOOLS:
+        _add_tool_command(tool_subparsers, tool)
+
+
+async def cmd_tool(args: argparse.Namespace) -> int:
+    kwargs = {
+        key: value
+        for key, value in vars(args).items()
+        if key not in {"command", "tool_name", "tool_handler"}
+    }
+    try:
+        result = await args.tool_handler(**kwargs)
+        if isinstance(result, str):
+            print(result)
+        else:
+            print(json.dumps(result, indent=2, default=str))
+        return 0
+    except Exception as e:
+        print(json.dumps({"status": "error", "message": str(e)}))
+        return 1
diff --git a/pyproject.toml b/pyproject.toml
index 8bb7eedc..4b784588 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,7 +47,7 @@ Repository = "https://github.com/openags/paper-search-mcp"
 Issues = "https://github.com/openags/paper-search-mcp/issues"
 
 [project.scripts]
-paper-search-mcp = "paper_search_mcp.server:main"
+paper-search-mcp = "paper_search_mcp.mcp:main"
 paper-search = "paper_search_mcp.cli:main"
 
 [tool.hatch.build.targets.wheel]
diff --git a/tests/test_acm.py b/tests/test_acm.py
index 79f34f2e..95d7b32e 100644
--- a/tests/test_acm.py
+++ b/tests/test_acm.py
@@ -45,9 +45,9 @@ def test_read_raises_not_implemented_without_key(self):
     def test_not_in_all_sources_without_key(self):
         """acm must NOT appear in ALL_SOURCES when the key is absent."""
         import importlib
-        import paper_search_mcp.server as srv_module
-        importlib.reload(srv_module)
-        self.assertNotIn("acm", srv_module.ALL_SOURCES)
+        import paper_search_mcp.api as api_module
+        importlib.reload(api_module)
+        self.assertNotIn("acm", api_module.ALL_SOURCES)
 
 
 class TestACMIsConfiguredWithKey(unittest.TestCase):
diff --git a/tests/test_server.py b/tests/test_api.py
similarity index 61%
rename from tests/test_server.py
rename to tests/test_api.py
index 292bae17..e0399eb8 100644
--- a/tests/test_server.py
+++ b/tests/test_api.py
@@ -1,28 +1,28 @@
-# tests/test_server.py
+# tests/test_api.py
 import unittest
 import asyncio
 import os
-from paper_search_mcp import server
+from paper_search_mcp import api
 
-class TestPaperSearchServer(unittest.TestCase):
+class TestPaperSearchApi(unittest.TestCase):
     def test_all_sources_include_new_platforms(self):
-        self.assertIn("dblp", server.ALL_SOURCES)
-        self.assertIn("openaire", server.ALL_SOURCES)
-        self.assertIn("citeseerx", server.ALL_SOURCES)
-        self.assertIn("doaj", server.ALL_SOURCES)
-        self.assertIn("base", server.ALL_SOURCES)
-        self.assertIn("zenodo", server.ALL_SOURCES)
-        self.assertIn("hal", server.ALL_SOURCES)
-        self.assertIn("ssrn", server.ALL_SOURCES)
-        self.assertIn("unpaywall", server.ALL_SOURCES)
+        self.assertIn("dblp", api.ALL_SOURCES)
+        self.assertIn("openaire", api.ALL_SOURCES)
+        self.assertIn("citeseerx", api.ALL_SOURCES)
+        self.assertIn("doaj", api.ALL_SOURCES)
+        self.assertIn("base", api.ALL_SOURCES)
+        self.assertIn("zenodo", api.ALL_SOURCES)
+        self.assertIn("hal", api.ALL_SOURCES)
+        self.assertIn("ssrn", api.ALL_SOURCES)
+        self.assertIn("unpaywall", api.ALL_SOURCES)
 
     def test_parse_sources_with_new_platforms(self):
-        parsed = server._parse_sources("dblp,doaj,base,zenodo,hal,ssrn,unpaywall,invalid")
+        parsed = api._parse_sources("dblp,doaj,base,zenodo,hal,ssrn,unpaywall,invalid")
         self.assertEqual(parsed, ["dblp", "doaj", "base", "zenodo", "hal", "ssrn", "unpaywall"])
 
     def test_search_arxiv(self):
         """Test the search_arxiv tool returns 10 results."""
-        result = asyncio.run(server.search_arxiv("machine learning", max_results=10))
+        result = asyncio.run(api.search_arxiv("machine learning", max_results=10))
         self.assertIsInstance(result, list, "Result should be a list")
         self.assertEqual(len(result), 10, "Should return exactly 10 results")
         for paper in result:
@@ -32,7 +32,7 @@ def test_search_arxiv(self):
     def test_download_arxiv_from_search(self):
         """Test downloading 10 arXiv papers based on search results."""
         # 先搜索 10 个结果
-        search_results = asyncio.run(server.search_arxiv("machine learning", max_results=10))
+        search_results = asyncio.run(api.search_arxiv("machine learning", max_results=10))
         self.assertEqual(len(search_results), 10, "Search should return 10 results")
 
         # 下载目录
@@ -42,10 +42,10 @@ def test_download_arxiv_from_search(self):
         # 下载每个搜索结果的 PDF
         for paper in search_results:
             paper_id = paper['paper_id']
-            result = asyncio.run(server.download_arxiv(paper_id, save_path))
+            result = asyncio.run(api.download_arxiv(paper_id, save_path))
             self.assertIsInstance(result, str, f"Result for {paper_id} should be a file path")
             self.assertTrue(result.endswith(".pdf"), f"Result for {paper_id} should be a PDF file path")
             self.assertTrue(os.path.exists(result), f"PDF file for {paper_id} should exist on disk")
 
 if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file
+    unittest.main()
diff --git a/tests/test_fallback.py b/tests/test_fallback.py
index f62fafac..cec5d562 100644
--- a/tests/test_fallback.py
+++ b/tests/test_fallback.py
@@ -2,16 +2,16 @@
 import asyncio
 from unittest.mock import patch, AsyncMock
 
-from paper_search_mcp import server
+from paper_search_mcp import api
 
 
 class TestDownloadWithFallback(unittest.TestCase):
     def test_repository_fallback_before_scihub(self):
-        with patch.object(server.arxiv_searcher, "download_pdf", side_effect=Exception("primary failed")), \
-             patch("paper_search_mcp.server._try_repository_fallback", new=AsyncMock(return_value=("/tmp/repo.pdf", ""))), \
-             patch("paper_search_mcp.server.SciHubFetcher.download_pdf", side_effect=AssertionError("Sci-Hub should not be called")):
+        with patch.object(api.arxiv_searcher, "download_pdf", side_effect=Exception("primary failed")), \
+             patch("paper_search_mcp.api._try_repository_fallback", new=AsyncMock(return_value=("/tmp/repo.pdf", ""))), \
+             patch("paper_search_mcp.api.SciHubFetcher.download_pdf", side_effect=AssertionError("Sci-Hub should not be called")):
             result = asyncio.run(
-                server.download_with_fallback(
+                api.download_with_fallback(
                     source="arxiv",
                     paper_id="1234.5678",
                     doi="10.1000/test",
@@ -22,12 +22,12 @@ def test_repository_fallback_before_scihub(self):
             self.assertEqual(result, "/tmp/repo.pdf")
 
     def test_unpaywall_fallback_after_repositories(self):
-        with patch.object(server.arxiv_searcher, "download_pdf", side_effect=Exception("primary failed")), \
-             patch("paper_search_mcp.server._try_repository_fallback", new=AsyncMock(return_value=(None, "repo failed"))), \
-             patch.object(server.unpaywall_resolver, "resolve_best_pdf_url", return_value="https://example.org/oa.pdf"), \
-             patch("paper_search_mcp.server._download_from_url", new=AsyncMock(return_value="/tmp/unpaywall.pdf")):
+        with patch.object(api.arxiv_searcher, "download_pdf", side_effect=Exception("primary failed")), \
+             patch("paper_search_mcp.api._try_repository_fallback", new=AsyncMock(return_value=(None, "repo failed"))), \
+             patch.object(api.unpaywall_resolver, "resolve_best_pdf_url", return_value="https://example.org/oa.pdf"), \
+             patch("paper_search_mcp.api._download_from_url", new=AsyncMock(return_value="/tmp/unpaywall.pdf")):
             result = asyncio.run(
-                server.download_with_fallback(
+                api.download_with_fallback(
                     source="arxiv",
                     paper_id="1234.5678",
                     doi="10.1000/test",
@@ -38,11 +38,11 @@ def test_unpaywall_fallback_after_repositories(self):
             self.assertEqual(result, "/tmp/unpaywall.pdf")
 
     def test_no_scihub_returns_oa_chain_error(self):
-        with patch.object(server.arxiv_searcher, "download_pdf", side_effect=Exception("primary failed")), \
-             patch("paper_search_mcp.server._try_repository_fallback", new=AsyncMock(return_value=(None, "repo failed"))), \
-             patch.object(server.unpaywall_resolver, "resolve_best_pdf_url", return_value=None):
+        with patch.object(api.arxiv_searcher, "download_pdf", side_effect=Exception("primary failed")), \
+             patch("paper_search_mcp.api._try_repository_fallback", new=AsyncMock(return_value=(None, "repo failed"))), \
+             patch.object(api.unpaywall_resolver, "resolve_best_pdf_url", return_value=None):
             result = asyncio.run(
-                server.download_with_fallback(
+                api.download_with_fallback(
                     source="arxiv",
                     paper_id="1234.5678",
                     doi="10.1000/test",
diff --git a/tests/test_ieee.py b/tests/test_ieee.py
index 61f4d9a7..e8469160 100644
--- a/tests/test_ieee.py
+++ b/tests/test_ieee.py
@@ -47,9 +47,9 @@ def test_not_in_all_sources_without_key(self):
         """ieee must NOT appear in ALL_SOURCES when the key is absent."""
         # Reload server module with key absent to get a clean ALL_SOURCES
         import importlib
-        import paper_search_mcp.server as srv_module
-        importlib.reload(srv_module)
-        self.assertNotIn("ieee", srv_module.ALL_SOURCES)
+        import paper_search_mcp.api as api_module
+        importlib.reload(api_module)
+        self.assertNotIn("ieee", api_module.ALL_SOURCES)
 
 
 class TestIEEEIsConfiguredWithKey(unittest.TestCase):
diff --git a/tests/test_tool_cli.py b/tests/test_tool_cli.py
new file mode 100644
index 00000000..38e9b013
--- /dev/null
+++ b/tests/test_tool_cli.py
@@ -0,0 +1,30 @@
+import asyncio
+import io
+import json
+import unittest
+from contextlib import redirect_stdout
+
+from paper_search_mcp import api, cli
+
+
+class TestToolCli(unittest.TestCase):
+    def test_build_parser_accepts_tool_command(self):
+        parser = cli.build_parser()
+        args = parser.parse_args(["tool", "search_papers", "query", "--max-results-per-source", "3"])
+        self.assertEqual(args.command, "tool")
+        self.assertEqual(args.tool_name, "search_papers")
+        self.assertEqual(args.query, "query")
+        self.assertEqual(args.max_results_per_source, 3)
+
+    def test_cmd_tool_runs_shared_api_function(self):
+        parser = cli.build_parser()
+        args = parser.parse_args(["tool", "sources"])
+        buffer = io.StringIO()
+        with redirect_stdout(buffer):
+            exit_code = asyncio.run(cli.cmd_tool(args))
+        self.assertEqual(exit_code, 0)
+        self.assertEqual(json.loads(buffer.getvalue()), {"sources": api.ALL_SOURCES})
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/test_unpaywall_source.py b/tests/test_unpaywall_source.py
index 4e73dbd5..1fcd1b19 100644
--- a/tests/test_unpaywall_source.py
+++ b/tests/test_unpaywall_source.py
@@ -3,19 +3,19 @@
 from datetime import datetime
 from unittest.mock import patch
 
-from paper_search_mcp import server
+from paper_search_mcp import api
 from paper_search_mcp.paper import Paper
 
 
 class TestUnpaywallSearchSource(unittest.TestCase):
     def test_search_unpaywall_empty_without_access(self):
-        with patch.object(server.unpaywall_resolver, "has_api_access", return_value=False):
-            result = asyncio.run(server.search_unpaywall("10.1000/test"))
+        with patch.object(api.unpaywall_resolver, "has_api_access", return_value=False):
+            result = asyncio.run(api.search_unpaywall("10.1000/test"))
         self.assertEqual(result, [])
 
     def test_search_unpaywall_empty_without_doi(self):
-        with patch.object(server.unpaywall_resolver, "has_api_access", return_value=True):
-            result = asyncio.run(server.search_unpaywall("machine learning"))
+        with patch.object(api.unpaywall_resolver, "has_api_access", return_value=True):
+            result = asyncio.run(api.search_unpaywall("machine learning"))
         self.assertEqual(result, [])
 
     def test_search_unpaywall_returns_one_record(self):
@@ -31,9 +31,9 @@ def test_search_unpaywall_returns_one_record(self):
             source="unpaywall",
         )
 
-        with patch.object(server.unpaywall_resolver, "has_api_access", return_value=True), \
-             patch.object(server.unpaywall_resolver, "get_paper_by_doi", return_value=paper):
-            result = asyncio.run(server.search_unpaywall("doi:10.1000/test"))
+        with patch.object(api.unpaywall_resolver, "has_api_access", return_value=True), \
+             patch.object(api.unpaywall_resolver, "get_paper_by_doi", return_value=paper):
+            result = asyncio.run(api.search_unpaywall("doi:10.1000/test"))
 
         self.assertEqual(len(result), 1)
         self.assertEqual(result[0]["source"], "unpaywall")