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Replace the split executable approval and sandbox resolution workflows with schema_version 2 and a YAML-driven execution.entries model. Resolve workspace, mount, executable, runtime, network, and resource settings into one config-scoped Applied Configuration snapshot protected by a user-only DACL and written with atomic replacement.
Reduce the public CLI to implicit server startup, show, and apply. Remove serve/check, executable and sandbox subcommands, and configuration override flags including --config, --lang, --transport, --path, and --runtime-root. Add migration diagnostics for every removed schema and command surface, and keep server preflight mandatory for both stdio and HTTP.
Update effective-policy compilation to validate the applied fingerprint, resolved paths, and executable hashes before startup. Preserve fail-closed behavior while allowing execution entries and runtime roots inside a development workspace to inherit that workspace capability without creating an impossible narrower ACL boundary.
Rewrite the README around the consolidated permission matrix and document configuration, application, store location, startup, transport-specific elevation, Python 3.14, PowerShell, and cmd usage. Align specifications, design, implementation plan, traceability, audit report, localization, publish scripts, and operational verification with the breaking schema.
Verification: Release build completed with zero warnings and errors; Agent.Core.Tests 104/104 and Agent.Planner.Tests 10/10 passed; administrator Windows Security/Recovery 56/56 and README operational 19/19 passed with no skips; published HTTP MCP completed a cmd/curl/venv-Python task with network deny and zero ACL, WFP, journal, backup, or process residue.
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