fix(agent-org): delete all runs for a root conversation

[ShiboSheng]

Problem

PR1 records exact Run-to-Session ownership and PR2 blocks fenced Agent Org runtime installation and submissions, but deleting an Agent Org Root still handles only one Run. A Root with historical and live Runs can therefore be rejected or partially handled instead of deleting the complete conversation safely.

Solution

Add a dedicated multi-Run Root deletion protocol that plans every Run from exact agent_org_run_sessions mappings, establishes the durable Root fence, cancels and quiesces starting/running/paused runtimes, rechecks topology, and removes all Run- and Session-owned SQLite state in one BEGIN IMMEDIATE transaction. Failed commits retain the fence and cancelled state for restart-safe retry; successful commits return a deduplicated Root/Worker receipt and perform runtime/cache/filesystem cleanup afterward.

The PR also adds bounded 1,024 Run/Session validation, rollback and concurrency coverage, two production HTTP E2E scenarios, and the existing rendered Tauri sidebar deletion regression for completed/running/paused Roots.

Potential risks

• This is a stacked Draft PR and requires PR2 (codex/issue-642-runtime-submission-defense) first.
• A non-cooperative runtime causes a bounded 10-second failure; the durable fence remains and deletion must be retried after the runtime stops.
• Filesystem cleanup occurs after the durable commit. Failures are logged and do not resurrect SQLite state. Persistent Shell Replay cleanup jobs remain intentionally scoped to a separate follow-up PR.
• Downgrading to a version that does not understand an unfinished deletion fence is unsupported.
• Repository-wide strict Clippy and rustfmt gates are currently blocked by pre-existing files outside this diff; PR-owned Rust files pass rustfmt, and no-deps Clippy shows only baseline warnings outside PR3 files.

Verification

• PASS — cargo test -p agent_core --lib state::commands::session::agent_org_delete_tests -- --nocapture (11/11)
• PASS — cargo test -p agent_core --lib (3189 passed, 0 failed, 2 ignored on clean rerun; first run had one transient SQLite lock in an unrelated sidebar test, which passed alone)
• PASS — cargo check -p e2e-test
• PASS — cargo run -p e2e-test -- --list (212 scenarios; both new scenarios registered)
• PASS — agent-org-multi-run-root-delete-production-command (5/5 checks)
• PASS — agent-org-multi-run-root-delete-rollback-retry (6/6 checks)
• PASS — existing agent-org-session-delete-ui.spec.mjs via isolated WDIO/Tauri (3/3)
• PASS — focused deletion receipt Vitest tests (5/5)
• PASS — pnpm run typecheck
• PASS — pnpm run check:circular
• PASS — changed-file rustfmt and Prettier checks
• PASS — git diff --check
• FAIL (baseline) — strict workspace Clippy stops on seven existing orgtrack_core warnings; no-deps checks contain no PR3-file warnings after fixes
• FAIL (baseline) — package rustfmt check reports existing Plan Approval, Shell Replay, and skills-loader formatting outside this diff

Scope and size

• 17 files; 3,291 additions and 1,618 deletions (4,909 raw lines)
• Production additions: 1,192
• Test/debug additions: 2,099
• Deleted old implementation: 1,618
• Mechanical-only movement: 0
• No IPC/wire shape, user-visible UI, dependency, or lockfile changes