First Time Setup Help - Expected File Structure?

[pt-oxford]

Hi All,

First of all I'm very excited to this out properly! Thank you so much for all the work that has gone into this!

I'm struggling to get things working at the moment - and clearly a user error - but would be very grateful for some help.
I've followed the Linux instructions provided, though having some issues:

git clone https://github.com/danielmiessler/PAI.git ~/.claude

this results in the following file structure

.claude
├──.claude
|    ├── agents
|    ├── commands
|    ├── hooks
|    │   └── lib
|    ├── Observability
|    │   ├── apps
|    │   └── scripts
|    ├── skills
|    │   ├── AlexHormoziPitch
|    │   ├── Art
|    │   └── ...
|    ├── tools
|    │   └── setup
|    └── voice-server
|        ├── macos-service
|        └── menubar
├── docs
│   └── images
├──.git
|    └── ...
└──...

After running the next command:

bash ~/.claude/.claude/tools/setup/bootstrap.sh

with

  🤖 PAI Setup Wizard
│
◆  Where should PAI be installed?
│  /home/USER/.claude

(Should I have changed this?)
I get the following changes to the file structure:

.claude
├──.claude
|    ├── agents
|    ├── commands
|    ├── hooks
|    │   └── lib
|    ├── Observability
|    │   ├── apps
|    │   └── scripts
|    ├── skills
|    │   ├── AlexHormoziPitch
|    │   ├── Art
|    │   └── ...
|    ├── tools
|    │   └── setup
|    └── voice-server
|        ├── macos-service
|        └── menubar
├── config            <--------
├── docs
│   └── images
├──.git
|    └── ...
├── history           <--------
├── skills            <--------
├── tools             <--------
├── voice-server      <--------
 |    └── logs
└──...

But these new directories are empty. And the command below doesn't work as there's no file to pull from in that directory.

cp ~/.claude/.env.example ~/.claude/.env

I assume it would have to be one of the following:

cp ~/.claude/.claude/.env.example ~/.claude/.env
cp ~/.claude/.claude/.env.example ~/.claude/.claude/.env

I've tried manually reading the SKILL.md file which loads up great.. but then no agents, skills etc are loaded up as they are in the wrong directories (?).

If anyone could clarify the expected file structure, or if there is a particular structure that is going to be used going forward.. I am more than happy to jump in and break things on my system, I'm just not quite getting this core aspect right.
Or if there is something I have missed that would fix this that would be amazing!

[pt-oxford]

Nevermind! Failed to grasp that I had to copy .claude over to my home directory!

[Gerkinfeltser]

I see you figured it out but:

I feel your pain friend. It took me some thrashing as well & I'm still not sure I have this right, but here's what's been working for me:

The Core Issue

It seems like you shouldn't name the root directory of PAI .claude, as you found it nests the extra .claude in the root .claude & is confusing/probably causes issues.

The Solution

What I've been doing is having ~/PAI-repo-root (or similar) as the actual PAI installation, then just symlinking the various necessary directories back to your ~/.claude directory. That way, any directory you start cc from will get all the things loaded.

Step-by-step:

# 1. Clone PAI to a proper location (NOT ~/.claude)
git clone https://github.com/danielmiessler/Personal_AI_Infrastructure ~/PAI-repo-root

# 2. Symlink the core directories to ~/.claude
ln -s ~/PAI-repo-root/.claude/skills ~/.claude/
ln -s ~/PAI-repo-root/.claude/agents ~/.claude/
ln -s ~/PAI-repo-root/.claude/settings.json ~/.claude/
# Add any other directories you need

# 3. Now run the bootstrap script
cd ~/PAI-repo-root
./setup.sh  # or whatever bootstrap method

Why This Seems to Work Better

Disclaimer: These are just my observations - could be totally wrong!

1. Separation of concerns: Your PAI config lives separately from Claude Code's internal .claude directory
2. No conflicts: The bootstrap script won't overwrite Claude Code's own structure
3. Clean updates: You can pull updates to PAI without affecting your active config
4. Git hygiene: Your PAI repo remains a clean git checkout

MCP Servers Note

Full disclosure: This is just what I've been doing and don't know if it's the right way! YMMV.

One thing to note: for any project directory (where you start cc from), if you want to use MCP servers you either have to:

1. Add them the normal CC way (project-specific)
2. Copy/symlink a setup .mcp.json into the project root:

# Option A: Global MCP setup (symlink)
ln -s ~/PAI-repo-root/templates/.mcp.json ~/.claude/

# Option B: Per-project setup
cp ~/PAI-repo-root/templates/.mcp.json /path/to/your/project/

Again, not sure if this is the "correct" approach - just what's been working for me!

The Key Takeaway (I think?)

In short, the extra layer is confusing & sort of contrary to what some of the setup process makes it sound like. The PAI documentation could maybe emphasize:

• ~/.claude = Claude Code's config directory (where CC looks)
• Your PAI repo = Source code for your personal infrastructure
• Use symlinks to connect them

This approach SEEMS to give you the best of both worlds: a clean PAI installation that integrates with Claude Code without the nested directory confusion. But again, what do I know!

---

Caveat: Honestly, if I'm wrong about this approach, someone please correct me! This is just what worked for me after some thrashing, and I'm still learning the PAI architecture myself. There might be better or more "official" ways to handle this setup!

[pt-oxford]

thanks for your help :) Will be trying this too!