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

Author: mnriem

README.md

@@ -341,7 +341,7 @@ block-beta
     style core fill:transparent,stroke:#e6a817
 ```
 
-Templates resolve top-down: the first match wins. Project-local overrides (`.specify/templates/overrides/`) let you make one-off adjustments for a single project without creating a full preset. Commands work differently — presets and extensions register their command files directly into agent directories (e.g., `.claude/commands/`), overwriting any earlier version. If no overrides or customizations exist, Spec Kit uses its core defaults.
+**Templates** are resolved at **runtime** — Spec Kit walks the stack top-down and uses the first match. Project-local overrides (`.specify/templates/overrides/`) let you make one-off adjustments for a single project without creating a full preset. **Commands** are applied at **install time** — when you run `specify extension add` or `specify preset add`, command files are copied into agent directories (e.g., `.claude/commands/`), replacing whatever was there before; the last-installed version is the one the agent sees. Commands are cleaned up on removal. If no overrides or customizations exist, Spec Kit uses its core defaults.
 
 ### Extensions — Add New Capabilities
 

presets/README.md

@@ -13,13 +13,15 @@ When Spec Kit needs a template (e.g. `spec-template`), it walks a resolution sta
 
 If no preset is installed, core templates are used — exactly the same behavior as before presets existed.
 
+Template resolution happens **at runtime** — nothing is copied; Spec Kit walks the stack on every lookup.
+
 For detailed resolution and command registration flows, see [ARCHITECTURE.md](ARCHITECTURE.md).
 
 ## Command Overrides
 
 Presets can also override the commands that guide the SDD workflow. Templates define *what* gets produced (specs, plans, constitutions); commands define *how* the LLM produces them (the step-by-step instructions).
 
-When a preset includes `type: "command"` entries, the commands are automatically registered into all detected agent directories (`.claude/commands/`, `.gemini/commands/`, etc.) in the correct format (Markdown or TOML with appropriate argument placeholders). When the preset is removed, the registered commands are cleaned up.
+Unlike templates, command overrides are applied **at install time**. When a preset includes `type: "command"` entries, the commands are registered into all detected agent directories (`.claude/commands/`, `.gemini/commands/`, etc.) in the correct format (Markdown or TOML with appropriate argument placeholders). When the preset is removed, the registered commands are cleaned up.
 
 ## Quick Start