[FEATURE] Support global prompt templates path (e.g., ~/.claude/prompts/)

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

The current workflow requires me to manually copy prompt template files to every project when using MCP integrations.
MCP servers can be registered globally with --scope user, making them accessible from any project. However, the @ file reference only searches within the current working directory and its subdirectories. This creates an inconsistency:

✅ MCP: Global scope supported (--scope user)
❌ Prompt templates: Project-local only

When using Atlassian MCP for Jira/Confluence, I want to maintain a single prompt template file with common queries (e.g., "show my assigned issues", "find pages that mentioned me"). But currently, I have to either copy this file to every project or use long absolute paths.

Proposed Solution

I'd like to be able to reference prompt template files from a global directory (e.g., ~/.claude/prompts/) regardless of the current working directory.
The interface should allow something like:
bash# File location: ~/.claude/prompts/atlassian.md

Usage from any project:

@atlassian.md show my morning routine
Or with a configuration in ~/.claude/settings.json:

{
  "promptPaths": ["~/.claude/prompts/"]
}

Alternative Solutions

Currently I work around this by:

Using absolute paths like @C:\Users\username\.claude\atlassian-prompts.md (verbose and OS-specific)
Creating symbolic links in each project directory (requires manual setup per project)
Copying the template file to every project (defeats the purpose of having a single source of truth)

Other tools solve this by:

Git has global config (~/.gitconfig) alongside project-local config
npm has global packages alongside project dependencies
MCP already supports this pattern with --scope user vs --scope project

Priority

Medium - Would be very helpful

Feature Category

Configuration and settings

Use Case Example

Workflow I want to achieve:

Register Atlassian MCP globally (one-time setup):

claude mcp add --transport sse atlassian --scope user https://mcp.atlassian.com/v1/sse

Create prompt template once at ~/.claude/prompts/atlassian.md:

## Morning Routine
   Show my assigned Jira issues in progress and Confluence pages that mentioned me this week
   
## My Issues  
   List my incomplete Jira issues by priority

Use from any project:

cd ~/project-a
   claude
   > @atlassian.md morning routine   # Works!
   
cd ~/project-b  
   claude
   > @atlassian.md morning routine   # Also works!

This would make MCP + prompt templates workflow seamless, especially for account-based integrations (Atlassian, GitHub, Notion, etc.) that are not project-specific.

Additional Context

Similar features in other tools:

VS Code: User-level snippets at ~/.config/Code/User/snippets/ work globally across all workspaces
Git: Global config (~/.gitconfig) vs local config (.git/config)
Claude CLI already has this pattern: claude mcp add --scope user vs --scope project

Technical considerations:

Search priority could be: project directory → user global directory (~/.claude/prompts/)
If same filename exists in both locations, project-local should take precedence (consistent with Git config behavior)
Cross-platform path handling needed: ~/.claude/ on macOS/Linux, %USERPROFILE%\.claude\ on Windows

Environment:

OS: Windows 11 (but this feature would benefit all platforms equally)
Claude CLI version: latest

Why this matters:
This feature would align the file reference behavior with the existing MCP --scope user concept, providing a consistent "global vs project" model across all Claude CLI features.