docs: Add Extensions & Presets section to README (#1898)

* docs: add Extensions & Presets section to README

Add a new 'Making Spec Kit Your Own: Extensions & Presets' section that covers:
- Layering diagram (Mermaid) showing resolution order
- Extensions: what they are, when to use, examples
- Presets: what they are, when to use, examples
- When-to-use-which comparison table
- Links to extensions/README.md and presets/README.md

* docs: clarify project-local overrides in layering diagram

Address review feedback: explain the project-local overrides layer
shown in the diagram, and adjust the intro to acknowledge it as a
third customization mechanism alongside extensions and presets.

* docs: Clarify template vs command resolution in README

- Separate template resolution (top-down, first-match-wins stack) from
  command registration (written directly into agent directories)
- Update Mermaid diagram paths to use <preset-id> and <ext-id>
  placeholders consistent with existing documentation

Addresses PR review feedback on #1898.

* docs: Clarify install-time vs runtime resolution for commands and templates

- README: label templates as runtime-resolved (stack walk) and commands
  as install-time (copied into agent directories, last-installed wins)
- presets/README: add runtime note to template resolution, contrast with
  install-time command registration

* docs: Address review — fix template copy wording, tighten command override description

- presets/README: clarify that preset files are copied at install but
  template resolution still walks the stack at runtime
- README: describe priority-based command resolution and automatic
  restoration on removal instead of vague 'replacing whatever was there'