New disableQuery flag and filterCommands hook wired through the session engine

What

A new disableQuery flag and a new filterCommands hook were added and threaded through several parts of the session engine:

• The main query-run loop now checks disableQuery right after session-start hooks; if set (alongside a new-turn or queued-input condition), it returns early without running the turn.
• Session resume/adopt logic now checks disableQuery before auto-resuming orphaned agents or workflows, and before prompting about a stale resume, skipping both when it's set.
• The command-registry gained a filterCommands option and a memoized helper to filter the command list by a predicate, for plugins or other consumers to narrow which commands are shown.
• The main session component now accepts and passes through both disableQuery and filterCommands into the session engine, command-registry service, and turn controller.

Why

Together these let something embedding or driving a session suppress normal query/turn execution and restrict which commands are available, useful for building restricted or specialized session modes.