fix(agent): preserve completed thought elapsed time

[qdivan]

Summary

• preserve a previously observed positive, finite Agent Thought elapsed_time when the final log for the same message_id reports 0 or omits the field
• continue accepting later positive, finite elapsed-time updates while rejecting booleans and non-finite values as authoritative durations
• add focused regression coverage for zero, missing, updated, non-finite, boolean, and distinct-message cases

Closes #39757.

Validation

• Baseline regression: 4 failed, 6 passed against the unpatched implementation
• PYTHONDONTWRITEBYTECODE=1 uv run --project api pytest -p no:cacheprovider -o addopts='' api/tests/unit_tests/core/workflow/nodes/agent/test_message_transformer.py -q (10 passed)
• uv run --project api --dev ruff check api/core/workflow/nodes/agent/message_transformer.py api/tests/unit_tests/core/workflow/nodes/agent/test_message_transformer.py
• uv run --project api --dev ruff format --check api/core/workflow/nodes/agent/message_transformer.py api/tests/unit_tests/core/workflow/nodes/agent/test_message_transformer.py
• git diff --check

Duplicate Check

Checked the live issue timeline, open and closed pull requests by issue number, affected symbols, paths, and behavior, plus the current canonical main at 72c20daa61adb2448caa02f7d4e807af35f6a84e. No equivalent active fix, merged fix, public implementation claim, assignment, or contribution lock was found. PRs #35301, #35574, and #35932 concern different UI or behavior boundaries.

Browser / Playwright

Not run. The regression is isolated to backend Agent log aggregation and is deterministically covered by unit tests. A full browser reproduction requires a configured Dify service, model/Agent plugin, and workflow; no frontend code is changed.