fix: surface swallowed errors across storage and MCP layers

[josephgoksu]

Summary

• task_store.go: Log corrupt JSON fields during scan instead of silently returning zero values. Covers 7 task fields, 3 clarify session fields, and 4 draft_state unmarshal sites.
• sqlite.go: Replace _, _ = db.Exec(ALTER TABLE ...) migration pattern with proper column-existence checks via pragma_table_info. Real DDL errors now get logged.
• policy/audit.go: Log corrupt input_json in both scanDecision and scanDecisionRows instead of silently dropping it.
• mcp/handlers.go: Log GetProjectRoot failures in explain and simplify handlers instead of silently using an empty base path.

Test plan

• go build ./... compiles
• make test-quick passes
• Verify via --verbose that corrupt JSON in DB now produces warning logs

[greptile-apps]

Greptile Summary

Replaced silent error swallowing with proper error logging across storage and MCP layers. Previously, JSON unmarshal failures, DDL migration errors, and GetProjectRoot failures were silently ignored, making debugging difficult.

Key improvements:

• task_store.go: 14 JSON unmarshal sites now log warnings instead of silently returning zero values
• sqlite.go: Migration logic now checks column existence via pragma_table_info before executing DDL, logging real errors
• policy/audit.go: Corrupt input_json fields now logged in both scan functions
• mcp/handlers.go: GetProjectRoot failures now logged in explain and simplify handlers

All changes follow Go error handling best practices by logging at appropriate levels (slog.Warn for data corruption, slog.Debug for expected failures) while preserving backward compatibility.

Confidence Score: 5/5

• This PR is safe to merge with minimal risk
• Changes are purely additive (error logging only), don't alter control flow or return values, follow Go conventions with appropriate log levels, and improve observability without breaking existing behavior
• No files require special attention

Important Files Changed

Filename	Overview
internal/mcp/handlers.go	Logs GetProjectRoot errors instead of silently ignoring them in explain and simplify handlers
internal/memory/sqlite.go	Replaced blind migration pattern with proper column-existence checks via pragma_table_info
internal/memory/task_store.go	Added error logging for 14 JSON unmarshal sites across tasks, plans, and clarify sessions
internal/policy/audit.go	Logs corrupt input_json in both scan functions instead of silently dropping it

_{Last reviewed commit: 010280b}