feat: diff-aware install — detect manifest changes and re-apply without --force

[danielmeppiel]

Problem

Today, apm install checks whether a primitive (MCP server, APM package, etc.) is already configured and skips it if so. This is correct for idempotency, but it means that if a user changes the configuration in apm.yml (e.g., updates env vars, changes a URL, modifies args), the change is silently ignored unless they pass --force.

This applies to all primitive types:

• Registry MCP servers (skip via check_servers_needing_installation)
• Self-defined MCP servers (skip via _check_self_defined_servers_needing_installation, added in fix: skip already-configured self-defined MCP servers on install #191)
• APM packages (skip via file collision detection)

The manifest (apm.yml) should be the source of truth. When config changes in the manifest, apm install should detect the drift and re-apply — without requiring --force.

Proposed behavior

1. On apm install, compare the manifest's declared configuration against the currently installed configuration.
2. If a primitive is already installed and the configuration matches, skip it (current behavior — ✓ already configured).
3. If a primitive is already installed but the configuration differs, re-apply it and show something like ✓ updated or ↻ reconfigured.
4. --force remains available for full overwrite/reset scenarios.

Context

This was discussed in #191 (PR comment thread). The PR correctly unified the skip behavior for self-defined MCP servers to match registry servers. This issue tracks the next step: making install diff-aware across all primitives.

Acceptance criteria

• apm install detects config drift for registry MCP servers
• apm install detects config drift for self-defined MCP servers
• apm install detects config drift for APM package files
• Clear CLI output distinguishes "already configured" vs "updated"
• Existing --force behavior is preserved

[danielmeppiel]

Related: #259 . This is the same story, the apm.yml should be the source of truth, and remediation actions (like version upgrades, removals, new packages, etc) need to be taken in order to make the installation truthful with apm install.