Resuming preserves the prior architectural analysis, dependency mapping, and conversation history, avoiding the cost of repeating an hour of valid work. Anthropic states that resuming by session ID restores the agent’s full prior context, including files read, analysis performed, and decisions made. ( https://code.claude.com/docs/en/agent-sdk/sessions )

However, the session represents historical knowledge rather than a repository snapshot. Because three files changed externally, the agent must be told which files are affected and directed to re-read them before relying on earlier conclusions. Anthropic clarifies that sessions persist the conversation, not the filesystem. ( https://code.claude.com/docs/en/agent-sdk/sessions ) Targeted re-analysis updates the stale portion of the agent’s model while retaining the nine unchanged files’ established context.

Option A discards valuable work even though most of the analyzed code remains unchanged. Option C is accurate but inefficient because it reprocesses all twelve files regardless of whether they changed. Option D is unsafe: the agent may continue reasoning from obsolete function signatures, dependencies, or control flows.

The continuation prompt should identify the changed files, summarize the merge’s purpose where known, and request a focused comparison against the earlier understanding. Any architectural conclusions affected by those changes should then be revised explicitly.

Official references/topics: Session Resume; Filesystem Versus Conversation State; Targeted Re-Analysis; Repository Change Awareness.