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.
