Currently, hlyr only supports a single global thoughts repository configured in ~/.config/humanlayer/humanlayer.json. This creates friction for users working across multiple organizational boundaries.

Use Case

I work on:

• Personal projects (thoughts repo in my personal GitHub org)
• Freelance projects for multiple clients (separate thoughts repos for each client)

I frequently switch between these projects throughout the day, and each needs to sync to a different thoughts repository.

Current Limitations

• Only one thoughtsRepo can be configured globally
• The --config-file workaround requires specifying the flag on every command
• Easy to accidentally commit thoughts to the wrong repository
• Soft-linking between different thoughts repos is error-prone and cumbersome

Proposed Solution

Add a profile/context system that allows:

1. Named profiles - Define multiple thoughts configurations (e.g., "personal", "client-acme", "client-globex")
2. Per-repo configuration - Store profile selection in a local file (e.g., .thoughts-profile)
3. Automatic switching - Commands like humanlayer thoughts sync automatically use the correct thoughts repo based on the current directory
4. Simple management - Commands to create, list, and switch profiles

Example Workflow

# One-time setup
humanlayer thoughts profile create personal --repo ~/thoughts-personal
humanlayer thoughts profile create client-acme --repo ~/thoughts-acme

# Per-project setup (stores in .thoughts-profile)
cd ~/projects/personal-app
humanlayer thoughts init --profile personal

cd ~/projects/acme-project  
humanlayer thoughts init --profile client-acme

# Normal usage - automatically uses correct repo
cd ~/projects/personal-app
humanlayer thoughts sync  # → syncs to ~/thoughts-personal

cd ~/projects/acme-project
humanlayer thoughts sync  # → syncs to ~/thoughts-acme

This would eliminate manual config file management and prevent cross-contamination between thoughts repositories.

Happy to submit a PR for this if you're open to the approach!