Execute multiline terminal input as one current-shell compound so intermediate prompts cannot complete queued work early. Preserve shell state and cover Bash and PowerShell grouping with regression tests.
Start local PTY shells in a new process session and make close() escalate from SIGTERM to SIGKILL when a foreground command refuses to exit. This keeps code_execution_tool reset from blocking indefinitely on stuck terminal processes.\n\nAdd regression coverage for closing a TERM-resistant shell and document the reset lifecycle contract.
Add comprehensive file-level DOX documentation across the repo and update directory AGENTS.md indexes. Many new `*.py.dox.md` files were added under api, helpers, tools, plugins, extensions, webui, and other dirs to document endpoint purpose, ownership, runtime contracts, work guidance, and verification. Several AGENTS.md files were created or updated (agents profiles, api, docker, extensions, helpers, plugins, skills, webui components, etc.) to list child DOX files and clarify documentation/work guidance. Also add example and bundled profile DOX files (agent0, default, developer, hacker, researcher) and minor updates to helpers/dirty_json.py and its tests. These changes improve on-disk documentation coverage and establish the convention that each direct runtime file should have a matching `*.dox.md` describing its contracts and verification steps.
