fix: count each API response once in speed and token metrics - #622

Merged from the jason/beta4-local-fixes Trellis build (compat-repair base):
bounded stdin reads in shared hooks (sirmalloc#590), research dispatch may write the
task research dir (sirmalloc#634), scoped archive commits (sirmalloc#622, sirmalloc#630), list filter
traversal (sirmalloc#631), remove-subtask link check (sirmalloc#632), hooks.local.json ignore
(sirmalloc#633).

…rds cover

With a speed window set, fix/speed-metrics-transcripts keeps the share of
a record's tokens that matches the share of its interval inside the
window, and sirmalloc#622 counts each response once through
its last record. Together, a response's share came from its last
record's interval alone, which can cover only part of the time the
response ran:

- A response that runs tools in parallel logs a tool result between its
  records, so its last record's interval starts at that result and
  covers only the end of the response. A window holding that end kept
  all or most of the response's tokens against only part of its time.
- A forked subagent's transcript opens with a copy of the response that
  spawned it. No user record comes before the copy there, so it has no
  interval, and as the response's last record it kept all of the
  response's tokens however little of the response the window held.

A record's share now comes from its response's time: the union of the
intervals of all of the response's records, in the main transcript and
its subagent transcripts, including records logged before the window. A
record with no interval takes the time of the response's other records,
and a response without any interval keeps all its tokens as before.
Records without a message id keep their own interval. The active
duration is unchanged.

Replaying 12 real transcripts at up to 2000 points each, 2.8% of the
30s-window renders with a speed read more than twice what that rule
gives (10.6% on one transcript; worst 1349.1 t/s against 73.6), and
0.65% of the 120s-window renders. With this change every render matches
it.

Upstream: weekly limit timers (sirmalloc#768), prompt cache miss widgets (sirmalloc#770), context window size env override (sirmalloc#352, sirmalloc#407), windowed speed fixes (sirmalloc#769, sirmalloc#771), separator/renderer fixes (sirmalloc#773), custom-command styling (sirmalloc#775), clickable cwd links (sirmalloc#744), account email from live credentials (sirmalloc#724), cache timer reported expiry + short toggle (sirmalloc#576, sirmalloc#592), claude-status lock (sirmalloc#635, sirmalloc#772), dedup token metrics (sirmalloc#622, sirmalloc#725, sirmalloc#735).
Not adopted: sirmalloc#765 terminal width from COLUMNS with fixed reserve - the fork keeps flexMode/compactThreshold and tmux pane priority.

Hand edits outside conflicts:
- README.md: kept fork Configure flex separator behavior bullet and older-updates details wrapper; dropped upstream Related Projects additions (claude-eta)
- AGENTS.md: kept fork terminal width wording (sirmalloc#765 not adopted)
- src/types/FlexMode.ts, src/tui/components/TerminalWidthMenu.tsx, src/tui/components/__tests__/TerminalWidthMenu.test.ts, src/tui/components/TerminalOptionsMenu.tsx, src/tui/components/__tests__/TerminalOptionsMenu.test.ts: restored, fork keeps terminal width settings
- src/tui/App.tsx, src/tui/components/index.ts, src/types/index.ts: re-wired terminal width menu and FlexMode export
- src/types/StatusJSON.ts: dropped fork duplicate prompt_cache key, upstream schema is a superset
- src/utils/terminal.ts: COLUMNS source gated on non-tmux so tmux pane width keeps priority
- src/widgets/WeeklyLimitTimer.ts, src/utils/usage-prefetch.ts, src/widgets/__tests__/WeeklyLimitTimer.test.ts: compat fix - fableUsage/fableResetAt -> weeklyFableUsage/weeklyFableResetAt
- src/widgets/ApiUsage.tsx: compat fix - Context Bar honors effective context window (override, clamp, 1.0M format); Weekly renders a valid value despite a session error
- src/widgets/__tests__/ApiUsage.localModelFallback.test.ts: output tokens no longer counted in context (upstream sirmalloc#730)
- src/utils/__tests__/renderer-flex-width.test.ts, src/utils/__tests__/renderer-ansi.test.ts, src/utils/__tests__/gradient.test.ts, src/utils/__tests__/renderer-separator-collapse.test.ts, src/utils/__tests__/config.test.ts, src/tui/__tests__/App.test.ts: fork deviation - fork width model (flexMode, 6-column full reserve, kept settings, Terminal Width menu entry)
- src/utils/__tests__/default-colors.test.ts: fork deviation - accept ansi256:/hex: defaults
- src/utils/__tests__/usage-prefetch.test.ts: fork deviation - weekly usage comes from the API, fork widget imports from ApiUsage
- src/widgets/__tests__/CurrentWorkingDir.test.ts, src/widgets/__tests__/CustomCommand.test.ts: Settings literal gains flexMode/compactThreshold
- src/utils/__tests__/context-window.test.ts, src/utils/__tests__/jsonl-metrics.test.ts: restored fork tests upstream dropped
- docs/test-retirements.md: ledger for the dev-reload snapshot-path and RemoteControlStatus glyph (sirmalloc#605) tests upstream replaced