Redesign file system to avoid conflicts: layered approach with project overrides and global defaults, proper upgrade process

prompts/orchestrate.md

@@ -2,13 +2,21 @@ You are the Orchestrator Driver. Your job is to act as a **state machine** for t
 
 ## Read These Files
 
-1. {project}/.agent-framework/AGENT.md — Check if Autopilot is enabled
-2. {project}/.agent-framework/RULES.md
+The Orchestrator reads files using a **layered approach** with a clear precedence:
+
+1. **Project overrides** (highest precedence): `{project}/.agent-framework/` — contains project-specific customizations
+2. **Global framework** (default): `~/.agent-framework/` — contains the base framework files
+
+**Precedence rule**: If a file exists in the project's `.agent-framework/` directory, the Orchestrator reads it from there. If it doesn't exist, the Orchestrator reads it from the global `~/.agent-framework/` directory.
+
+Specifically:
+1. {project}/.agent-framework/AGENT.md (if exists — project override) OR ~/.agent-framework/AGENT.md (global default)
+2. {project}/.agent-framework/RULES.md (if exists — project override) OR ~/.agent-framework/RULES.md (global default)
 3. ~/.agent-framework/config.md — Global framework configuration (VRAM, model settings)
-4. {project}/.agent-framework/AGENT.md (if exists — for model override)
-5. {project}/.agent-framework/prompts/workflow.md — The State Machine
-6. Any existing files under {project}/tasks/
-7. {project}/.agent-framework/scripts/vram_detect.sh — VRAM detection script (if exists)
+4. {project}/.agent-framework/prompts/*.md (if exists — project overrides) OR ~/.agent-framework/prompts/*.md (global default)
+5. {project}/.agent-framework/contracts/*.md (if exists — project overrides) OR ~/.agent-framework/contracts/*.md (global default)
+6. {project}/.agent-framework/scripts/*.sh (if exists — project overrides) OR ~/.agent-framework/scripts/*.sh (global default)
+7. Any existing files under {project}/tasks/
 
 ## VRAM Detection