Fix terminal worktree cleanup and token reporting

[nickbeau]

Spec References

• SPEC.md Section 8.5: terminal tracker state stops running workers and cleans the workspace.
• SPEC.md Section 8.6: startup and terminal workspace cleanup semantics.
• SPEC.md Section 13.5: token accounting must prefer absolute totals, ignore delta/generic payloads, and track deltas from last reported totals.
• SPEC.md Section 15.1/15.2: workspace containment and subprocess safety remain mandatory.
• SPEC.md Section 17.2, 17.4, 17.5, and 17.6: conformance coverage for workspace cleanup, reconciliation, protocol usage extraction, and token/rate-limit observability.

Summary

This change tightens terminal cleanup, token accounting, and Git worktree preparation reliability for Symphony's v1 orchestrator.

Terminal Worktree Cleanup

• Persists terminal stop intent before canceling live issue workers, so the runner can reliably observe RunStopReasons.Terminal and the CleanupWorkspaceOnStop flag.
• Cleans worktrees for tracked retrying issues when GitHub reports the issue has moved to a configured terminal state such as Closed.
• Releases retry queue entries and active dispatch claims for retrying issues that become terminal.
• Records terminal cleanup metadata on workspace records when cleanup succeeds or the workspace is already absent.

Token Reporting

• Stops treating ordinary per-event usage maps as cumulative token totals.
• Continues accepting absolute usage payloads such as thread/tokenUsage/updated, total_token_usage, totalTokenUsage, token_usage, and tokenUsage.
• Still accepts a nested usage map when the event itself is an absolute token usage update.
• Resets LastReported*Tokens when a retry run starts a fresh agent attempt so new absolute session totals are counted correctly without losing the aggregate run totals.

Git Worktree Config Lock Fix

• Creates new per-issue worktree branches with git worktree add --no-track -b ... so Git does not attempt to write upstream branch configuration.
• Serializes shared-clone Git mutations inside the host process to reduce .git/config and worktree metadata contention when multiple issues dispatch concurrently.
• Avoids unnecessary git remote set-url origin ... calls when the shared clone already points at the configured remote.
• Flushes Git redirected output before checking command results.

Documentation

• Updates README.md to describe retrying terminal workspace cleanup and absolute-only token totals.
• Updates docs/UserGuide.md to document terminal retry cleanup, token accounting behavior, and upstream-free worktree branch creation.

Tests

• dotnet test tests/Symphony.Integration.Tests/Symphony.Integration.Tests.csproj --filter "WorkspaceManagerTests|OrchestrationTickServiceTests|CodexAgentRunnerTests"
• dotnet test

Full suite result: 13 core tests passed, 119 integration tests passed, 1 real GitHub integration test skipped because it is gated by opt-in credentials.

Notes

• The pre-existing untracked .claude/ directory was intentionally not staged.
• No migrations were required.

[Copilot]

Pull request overview

This PR tightens Symphony’s v1 orchestrator behavior around terminal workspace cleanup, absolute-only token usage accounting, and safer/more reliable Git worktree preparation under concurrent dispatch.

Changes:

• Persist terminal stop intent before canceling live runs; extend terminal cleanup to tracked retrying issues (including releasing retry/claim state and recording cleanup metadata).
• Token accounting now ignores generic per-event usage maps except for explicit absolute token-usage update events, and resets “last reported” totals when a retry starts a fresh attempt.
• Git worktree creation now uses upstream-free branches (--no-track) and serializes shared-clone Git mutations to reduce .git/config contention.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/Symphony.Integration.Tests/WorkspaceManagerTests.cs	Adds coverage ensuring worktree branches don’t configure upstream tracking; updates git helper to assert nonzero exit codes.
tests/Symphony.Integration.Tests/OrchestrationTickServiceTests.cs	Adds integration tests for persisting terminal stop state pre-cancel, retry workspace cleanup on terminal transition, and token “last reported” reset on retry attempt restart.
tests/Symphony.Integration.Tests/CodexAgentRunnerTests.cs	Adds tests verifying generic usage is ignored on ordinary events but accepted for absolute token usage update events.
src/Symphony.Infrastructure.Workspaces/GitWorktreeWorkspaceManager.cs	Adds per-shared-clone locking; switches new worktree branch creation to --no-track; avoids redundant remote set-url calls; improves process output flushing.
src/Symphony.Infrastructure.Agent.Codex/CodexAgentRunner.cs	Restricts usage parsing to absolute token usage update contexts; continues accepting known absolute total token payload shapes.
src/Symphony.Host/Services/OrchestrationTickService.cs	Passes instanceId into tracked-issue state refresh to support terminal retry cleanup/claim release.
src/Symphony.Host/Services/OrchestrationTickService.Reconciliation.cs	Persists stop intent before attempting to stop live execution, enabling runners to observe terminal stop semantics reliably.
src/Symphony.Host/Services/OrchestrationTickService.Persistence.cs	Adds tracked terminal cleanup for retrying issues during cache refresh; releases retry queue/claim state; records cleanup metadata.
src/Symphony.Host/Services/OrchestrationTickService.Dispatch.cs	Resets SessionId and last-reported token totals when re-dispatching a retrying run as a fresh attempt.
docs/UserGuide.md	Documents absolute-only token accounting and terminal cleanup behavior for retrying issues; notes upstream-free worktree branches and serialized Git mutations.
README.md	Updates high-level runtime behavior summary for retrying terminal cleanup and absolute-only token totals.

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