Update MCP docs

[atharvadeosthale]

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[greptile-apps]

Greptile Summary

This PR updates all MCP server documentation across 13 files to reflect the new auto-registration model: explicit service flags (--users, --databases, --sites, etc.) are removed from every config snippet, the "Command-line arguments" section is replaced with a "How it works" description of the two-tool compact workflow, and the now-obsolete "Enable other API MCP tools" info boxes are removed throughout.

• There is a parallel, older set of MCP docs at src/routes/docs/tooling/mcp/ (cursor, claude-code, claude-desktop, opencode, vscode, windsurf, and api) that was not updated. Those pages still show the flag-based configuration (e.g. --users) and link to a #command-line-arguments anchor that still exists in the old API page but contradicts the new auto-registration behavior. Users who reach either the old tool pages or the old API reference will get instructions that are now incorrect.

Confidence Score: 4/5

Safe to merge after the parallel old docs set at src/routes/docs/tooling/mcp/ is brought in sync with the new auto-registration model.

All 13 changed files are correctly and consistently updated. The one P1 concern is that a second, live docs tree was missed and still instructs users to add flags that the new server no longer requires, which could break existing setups or confuse users who land on the old pages.

src/routes/docs/tooling/mcp/ (entire directory — old API page and all tool sub-pages need the same flag-removal and section-rewrite applied here)

Important Files Changed

Filename	Overview
src/routes/docs/tooling/ai/mcp-servers/api/+page.markdoc	Replaces "Command-line arguments" section with "How it works" explanation of the new two-tool architecture; updates the "Customizable tools" bullet to "Automatic service discovery"
src/routes/integrations/mcp-claude/+page.markdoc	Removes --users flag from config snippet and drops the explanatory paragraph referencing command-line arguments; Claude Code CLI command updated to match
src/routes/integrations/mcp-cursor/+page.markdoc	Removes --users flag from Cursor config snippet and drops the explanatory paragraph about command-line arguments
src/routes/integrations/mcp-windsurf/+page.markdoc	Removes --databases and --users flags from Windsurf config snippet and drops the explanatory paragraph
src/routes/docs/tooling/ai/ai-dev-tools/windsurf/+page.markdoc	Removes --databases and --users flags (Windsurf had two) and the "Enable other API MCP tools" info box
src/routes/docs/tooling/ai/ai-dev-tools/cursor/+page.markdoc	Removes --users flag from the JSON config block and removes the "Enable other API MCP tools" info box linking to command-line-arguments docs
src/routes/docs/tooling/ai/ai-dev-tools/claude-code/+page.markdoc	Removes --users from inline JSON command and removes the "Enable other API MCP tools" info box
src/routes/docs/tooling/ai/ai-dev-tools/claude-desktop/+page.markdoc	Removes --users flag and the "Enable other API MCP tools" info box
src/routes/docs/tooling/ai/ai-dev-tools/opencode/+page.markdoc	Removes --sites flag (different default than most other pages which used --users) and the info box
src/routes/docs/tooling/ai/ai-dev-tools/vscode/+page.markdoc	Removes --sites flag and the "Enable other API MCP tools" info box
src/routes/docs/tooling/ai/ai-dev-tools/antigravity/+page.markdoc	Removes --users flag from config; no info box was present in this page
src/routes/docs/tooling/ai/ai-dev-tools/emergent/+page.markdoc	Removes --users flag and the "Enable other API MCP tools" info box
src/routes/docs/tooling/ai/ai-dev-tools/zenflow/+page.markdoc	Removes --sites flag from the Zenflow config block

_{Reviews (3): Last reviewed commit: "add note about available tools" | Re-trigger Greptile}