Add isolated command execution - #12

What changed

• Add an explicit Run isolated path that executes exact composer input in a child Bash process.
• Keep persistent Send for state-carrying shell commands and warn on common strict-mode prologues.
• Record execution mode on command cards, preserve it across reruns and saved transcripts, and migrate existing Room data as persistent.
• Document the remaining persistent-shell recovery and running-command input boundaries.

Why

A transcript command that enabled set -euo pipefail could terminate the persistent Bash shell after a failure before Threadline emitted its completion marker. Treating every command as isolated would prevent that failure but would also break persistent cd, exports, aliases, and functions.

The explicit mode keeps both contracts honest. An isolated failure reports the child status through the transcript while the outer shell remains available, including when the outer shell already has errexit enabled.

User impact

Script-like strict-mode commands can fail without dropping the SSH session when run isolated. Persistent shell behavior remains available when state changes are intentional.

Validation

• ./gradlew --no-daemon test lint assembleDebug assembleRelease
• Complete API 35 connected Android suite
• Production Android SSH integration suite against the disposable OpenSSH fixture using password and encrypted imported-key authentication
• Room v4-to-v5 migration and saved-transcript round trip
• Diff checks and high-confidence leak scan