Stream Planner tool calls from their own start and end, including Atomic's own tools

[lavaman131]

A Planner turn looks frozen in Chat. A tool row only appears once the model has finished writing its input, and only settles when the harness finishes the whole model step, so its duration covers the step instead of the tool. Under HARNESS=atomic, Atomic's builtin, extension, workflow and subagent tools (bash, read, workflow, subagent…) never reach Chat at all. If they did, the fixed PLANNER_TOOL_NAMES check would abort the turn.

This PR fixes the data side only. The chat presentation belongs to @MaggieAppleton's design work (#296, #162), so apps/web is unchanged and every protocol addition is optional.

What changes

• Protocol (packages/protocol/chat.d.ts, all optional): Activity.startedAt (server time when the tool's input began), Activity.refused, and Turn.startedAt in milliseconds. A client that ignores them keeps working.
• Tool rows from the tool's own start and end (apps/server/src/chat/service.ts):
  • A row opens on tool-input-start.
  • It settles when the tool itself finishes. HarnessAgent buffers host-tool results until step end, so agents.ts wraps execute to report completion straight away, and the buffered part then finds the row already settled.
  • Partial output updates the running row.
  • Running rows are marked failed when a turn ends or a room is restored.
• Redaction (chat/activity.ts): args and results are truncated to 4,000 characters, with token, password and API-key fields and ghp_ / github_pat_ / sk- / Bearer values masked. read_reference output stays private.
• Atomic's own tools (harness/atomic/adapter.ts, session.ts, full.ts):
  • tool_execution_start/update/end and tool-call input streaming become stream parts for tools Atomic runs itself. Nested subagent calls stay under their parent row.
  • A full session's allowed set is its running turn's active tools.
  • copilot-sdk and pi still fail closed on any tool outside their fixed set (regression test).
• Reasoning is deliberately not sent to clients. It can quote read_reference content that is private to the Planner, and whether to show it is a design call for Show Chopin's work as live stages with inspectable tools #296.

Overlap with #296

Both PRs touch Chat.Turn in chat.d.ts, where #296 adds entryOffset, and the two chat.turn = {…} literals in service.ts, which this PR replaces with begin(handle). Both also append tests to e2e/harness.e2e.ts. The changes don't conflict in meaning. I suggest merging #296 first; I'll then rebase and add entryOffset to begin().

Verification

Real GitHub, githubnext/pdd-demo, HARNESS=atomic, final build, with main's UI unchanged. Atomic's builtin Bash row appears live, then settles at 4.9s for sleep 4: its own duration, not the turn's. The server log has no boundary failure.

• bun run e2e e2e/harness.e2e.ts e2e/smoke.e2e.ts e2e/responsive-activity.e2e.ts: 28 passed. The new wire tests record WebSocket frames: the busy state comes before any text, the tool row settles at its own ~2.5s end inside a 7.5s turn, and a reload mid-turn restores the running row and turn start from history without reasoning.
• bun test: 3685 pass, 3 skip, 0 fail. This covers translate cases for input streaming, own-end settlement, boundary failures and reasoning privacy, plus the Atomic tool_execution_* and input-streaming adapter cases.
• bun run types and bun run ci pass, with no new Impeccable findings.

Refs #306

Assistant-workflow: goal (run 1e1a9fe2-7263-4372-9eb3-31c679ccb69e), finished inline
Assistant-duration: 3h15m converged, estimated 2h30m
Assistant-verification: bun test passed: 3685 tests, 0 fail
Assistant-verification: playwright e2e passed: harness, smoke, responsive-activity, 28 passed
Assistant-verification: bun run types and bun run ci passed
Assistant-verification: real GitHub QA passed: pdd-demo, HARNESS=atomic, builtin Bash live and settled at 4.9s for sleep 4, no boundary failure
User-preference: Don't overlap teammates' in-flight UI work; leave chat, composer and design changes to Maggie's design track (#296)
User-preference: Don't show Planner reasoning where it conflicts with Maggie's design
Co-authored-by: Alex Lavaee lavaman131@github.com