* CLI: clarify config vs configure descriptions
* CLI: improve top-level command descriptions
* CLI: make direct command help more descriptive
* CLI: add commands hint to root help
* CLI: show root help hint in implicit help output
* CLI: add help example for command-specific help
* CLI: tweak root subcommand marker spacing
* CLI: mark clawbot as subcommand root in help
* CLI: derive subcommand markers from registry metadata
* CLI: escape help regex CLI name
The initial fix using snapshot.parsed broke configs with $include directives.
This commit adds a new 'resolved' field to ConfigFileSnapshot that contains
the config after $include and ${ENV} substitution but BEFORE runtime defaults
are applied. This is now used by config set/unset to avoid:
1. Breaking configs with $include directives
2. Leaking runtime defaults into the written config file
Also removes applyModelDefaults from writeConfigFile since runtime defaults
should only be applied when loading, not when writing.
Fixes#6070
The config set/unset commands were using snapshot.config (which contains
runtime-merged defaults) instead of snapshot.parsed (the raw user config).
This caused runtime defaults like agents.defaults to leak into the written
config file when any value was set or unset.
Changed both set and unset commands to use structuredClone(snapshot.parsed)
to preserve only user-specified config values.
