Add --fresh-logs flag and fresh_logs config to truncate logs on start

[hiyamamo]

Summary

• Logs grow by appending across runs with no CLI-side cleanup (only the MCP truncate_log tool, per ログ肥大対策: truncate オプションまたはローテーション #36). ws-dev server --fresh-logs — or fresh_logs: true in the repo's config entry — now truncates every *.log in the log dir at start.
• Ordering is deliberate: truncation happens after the prior server is stopped (nothing is writing to the logs) and before setup runs, so a fresh run's logs contain only that run.
• In background mode the flag passes through to the detached child. The child truncating its own server.log is safe because the parent opened it with O_APPEND (writes reposition to the new EOF).
• Non-*.log files in the log dir are untouched; a missing log dir is a no-op.
• SKILL.md / README / CLAUDE.md updated (flag, config key, and a note that logs otherwise append forever).

Closes #36

Test plan

• New TestTruncateLogs: empties *.log, leaves other files alone, missing dir is a no-op
• fresh_logs parsing asserted in the existing config round-trip test
• make check passes

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