Mcp server only has two entry points now missing linkedin, deepresearch etc

TL;DR

Upgrade exa-mcp-server to 3.0.8 or 3.0.9 and change the flag syntax: drop the double dash and use a single tools= argument. The old --tools syntax silently exposes only two tools.

The problem

exa-mcp-server only exposes web_search_exa and get_code_context_exa even when all 7 tool names are passed. Linkedin search, deep researcher, crawling, and company research tools are gone.

Fix it

1. Upgrade the package:

   npm i -g exa-mcp-server@3.0.9

   Success check: the installed version is 3.0.8 or newer.

2. Change the flag syntax from --tools to tools=:

   "args": ["-y", "exa-mcp-server", "tools=web_search_exa,get_code_context_exa,crawling_exa,company_research_exa,linkedin_search_exa,deep_researcher_start,deep_researcher_check"]

   Success check: all 7 tools appear in the MCP tool list.

3. For remote MCP servers, pass ?tools=[comma-list] on the URL instead. Success check: the remote tool list shows all requested tools.

4. Temporary workaround before the fix: pin exa-mcp-server@2.0.5. Success check: tools reappear, but upgrade when you can.

When this applies

• exa-mcp-server 3.0.x showing only 2 tools despite --tools with all names.
• Missing linkedinsearchexa, deepresearcher*, crawlingexa, companyresearch_exa.

When it does not apply

• Tools missing on 2.x versions; that is a different configuration problem.
• The MCP client itself cannot list tools at all.

Compatibility

• exa-mcp-server npm package 3.0.8/3.0.9 (fixed). Affected: early 3.0.x.
• Workaround: pin 2.0.5.

Variant phrasings

• exa-mcp-server only two tools
• exa mcp missing linkedin deepresearch
• exa-mcp-server tools flag not working

Why it happens

Version 3.0 changed the CLI flag parsing: the double-dash --tools form stopped being recognized, so the server fell back to its default two tools. The single tools= form is parsed correctly in 3.0.8+.

Edge cases

• Quote the comma list if your MCP client config splits on commas.
• Remote URL form needs URL-encoded commas in some clients.

In gh:exa-labs/exa-mcp-server#66 (https://github.com/exa-labs/exa-mcp-server/issues/66), the question was: Since early in the month, exa-mcp-server only exposes websearchexa and getcodecontext_exa even when passing --tools with all 7 tool names - company research, crawling, linkedin search, deep researcher tools are gone. The verified resolution: Collaborator theishangoswami: fixed in npm package 3.0.8/3.0.9. The flag syntax changed: drop the double dash and use a single 'tools=' argument, e.g.