fix(conversation-store): msgIdx collision merges messages across turns + reconcile drops thinking-only messages

Root cause of tool-calls-in-thinking bug: append() assigns msgIdx as a LOCAL
index (reset to 0 per call), but load() grouped chunks by msgIdx alone. Since
the orchestrator persists messages one at a time (append([user]) at turn start,
then append([assistant, ...toolResults]) per step), all single-message appends
share msgIdx=0 and collapse into one giant user-role message. The model loses
its prior assistant responses and tool-call history, falls back to text-based
tool-call syntax inside reasoning_content, and the turn ends with finish_reason
stop (no structured tool_calls detected).

Fix 1 (store.ts load()): split message boundaries on role change too, not just
msgIdx. Handles the alternating user/assistant/tool pattern correctly.

Fix 2 (reconcile.ts hasContent): include thinking chunks as valid content so
thinking-only assistant messages are not silently dropped on load. The buggy
seq-14 output (assistant, thinking-only) was being deleted by reconcile,
destroying evidence of the bug.

Verified: load() on the affected conversation now produces 9 correct messages
(was 3 merged). All 1999 tests pass. See notes/tool-call-in-thinking-bug.md.

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