MCP Profile Management - Implementation Question

[Gerkinfeltser]

Hi, I'm trying to understand how the MCP profile management system described in the CONSTITUTION is supposed to work in practice, and I've run into some confusion.

The Situation

The CONSTITUTION (lines 1180-1212) documents an MCP profile management system:

${PAI_DIR}/MCPs/swap-mcp              # Show current profile
${PAI_DIR}/MCPs/swap-mcp chrome-enabled  # Switch to profile

I found this system in my PAI installation - full MCPs/ directory with swap-mcp.sh, mcp-registry.json, profile configs. It actually works when I'm working from the PAI/.claude/ directory.

Then I checked the public repo. The system isn't there. No MCPs/ directory, no swap-mcp script, no registry. Just .mcp.json.

PAI must have created this for me at some point while I wasn't paying close attention. The CONSTITUTION describes it, so PAI built it.

What Exists Where

Public repo:

• .claude/.mcp.json - Template with example configs
• CONSTITUTION describing the MCPs/ system (lines 1180-1212)
• settings.json with enableAllProjectMcpServers: true

My installation (auto-generated by PAI):

• PAI/.claude/MCPs/ directory
• swap-mcp.sh script
• mcp-registry.json with profiles
• mcp-profile.txt tracking active profile

Also relevant:

• statusline-command.sh has a whole MCP display section (lines 59-67, 201-262, 269). It reads mcpServers from settings.json and formats/displays active MCP names in the statusline. This suggests the MCP system was designed as an integrated part of PAI, not just documentation.

The Technical Confusion

Claude Code reads MCP configs from:

1. ~/.claude.json (system-level)
2. .mcp.json in project root (via enableAllProjectMcpServers: true)

PAI's .mcp.json lives at ~/.claude/.mcp.json. When PAI is installed to ~/.claude/, this is the .claude directory itself, not a project root. I tried adding it explicitly:

"enableAllProjectMcpServers": true,
"enabledMcpjsonServers": ["${PAI_DIR}/.mcp.json"]

The MCPs in that file don't get loaded.

The .mcp.json template has other issues:

• HTTP-based servers (httpx-mcp.danielmiessler.workers.dev, content-mcp, daemon, Foundry, naabu) - these are your personal Cloudflare Workers and APIs, right? Claude Code only supports stdio protocol, so these won't work for other users.
• Some stdio servers that could work (brightdata, stripe, Ref, apify, playwright)

Questions

1. Is the MCPs/ profile system part of your private setup? The CONSTITUTION documents it, but it's not in the public repo. Is this aspirational documentation, or just not pushed yet?

2. How should .mcp.json be used? A few possibilities:

   • Template that users manually migrate to ~/.claude.json?
   • Copied/symlinked to each project's root directory?
   • Some automated process I'm missing?

3. The HTTP-based MCP servers - I assume these are your personal infrastructure that won't work for other users? Should these be removed from the template, or are they just examples?

4. Does the workspace root requirement matter? The auto-generated MCPs/ system works when I'm working from PAI/.claude/ as my project directory, but that doesn't seem like the intended use case.

What I'm Actually Trying to Figure Out

Profile-based MCP management seems genuinely useful - swap between "research mode" (web scraping tools) and "dev mode" (GitHub/Supabase tools) without manually editing configs.

The main question: how does this work given Claude Code's requirement that .mcp.json be in the workspace root? Does PAI's .mcp.json need to be symlinked to each project, or is there a different approach?

The fact that the auto-generated swap-mcp system fooled me into thinking it was vanilla PAI is testament to how well PAI works - it built something coherent enough that I didn't realize it wasn't part of the original system. I'm curious about the intended architecture rather than whether the auto-generated version is "correct."

---

Environment: Claude Code on WSL2/Ubuntu

[danielmiessler]

Please refer to this major change coming to the repo that should address your issues. If it doesn't please resubmit. Thank you for the work!

#222

[jontstaz]

Hi @danielmiessler , I'm having the exact same thoughts as OP about this and after reading #222 the questions remain, namely about how to handle the ~/.claude/.mcp.json and ~/.claude.json . How do you handle this right now? I have my own global MCP servers in ~/.claude.json and obviously PAI has its MCP servers defined in ~/.claude/.mcp.json which means they are only accessible/usable when working from within ~/.claude which is obviously not ideal. So right now, in this current version, how are we meant to handle this in the correct way?

[danielmiessler]

When I was using MCPs I put them in ~/.claude via a .mcp.json file.

…

On Sat, Dec 20, 2025 at 7:46 PM, jontstaz < ***@***.*** > wrote: Hi @ danielmiessler ( https://github.com/danielmiessler ) , I'm having the exact same thoughts as OP about this and after reading #222 ( #222 ) the questions remain, namely about how to handle the ~/.claude/.mcp.json and ~/.claude.json . How do you handle this *right now* ? I have my own global MCP servers in ~/.claude.json and obviously PAI has its MCP servers defined in ~/.claude/.mcp.json which means they are only accessible/usable when working from within ~/.claude which is obviously not ideal. So right now, in this current version, how are we meant to handle this in the correct way? — Reply to this email directly, view it on GitHub ( #168 (reply in thread) ) , or unsubscribe ( https://github.com/notifications/unsubscribe-auth/AAAMLXWZIC2S6V2D5SLITFD4CYJZXAVCNFSM6AAAAACOMSDSU6VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTKMZQHA2TOOI ). You are receiving this because you were mentioned. Message ID: <danielmiessler/Personal_AI_Infrastructure/repo-discussions/168/comments/15308579 @ github. com>

[jontstaz]

So you didnt use them anywhere but when working in ~/.claude? Because .mcp.json is not universal

[Gerkinfeltser]

Yeah, .mcp.json only works in a project's root from what I understand. For global items the array is contained in ~/.claude.json which also contains a lot of other settings unfortunately. Its pretty annoying. Anyway, I'll wait and see how the new system flushes out. 👍