refactor: use mark_dirty() method instead of direct attribute assignment

[dharshan-X]

Replaces all direct assignments to session.history_dirty = True with the encapsulated session.mark_dirty() method call to properly enforce the performance semantics documented in the Session dataclass. This improves encapsulation.

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PR created automatically by Jules for task 7680221199825390300 started by @dharshan-X

Summary by CodeRabbit

• Refactor
  • Enhanced internal session state handling mechanisms for improved code consistency and maintainability across multiple components.

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ℹ️ Recent review info

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Run ID: d1f5d536-227a-43cf-9370-b88af00f2396

📥 Commits

Reviewing files that changed from the base of the PR and between 944da3f and b2b7549.

📒 Files selected for processing (6)

• agent.py
• bot.py
• cli.py
• commit_message.txt
• desktop/api_bridge.py
• prompt_builder.py

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Walkthrough

This PR refactors session dirty-flag tracking by replacing 18 direct assignments to session.history_dirty = True with calls to session.mark_dirty() across agent message handling, cancel handlers, and prompt-building workflows. No public APIs or logic flow changed.

Changes

Session Dirty Marking Method Refactor

Layer / File(s)	Summary
Agent message history operations agent.py	After appending tool results, user messages, resumed tool calls, assistant rounds, and resolving or denying confirmations, the agent now calls session.mark_dirty() instead of direct attribute assignment. Seven sites updated across _append_tool_result, _turn_state, _execute_unanswered_tool_calls, _append_assistant_round, _finalize_or_request_more_work, resolve_confirmations, and deny_confirmations.
Cancel and denial handlers bot.py, cli.py, desktop/api_bridge.py	Command-line, bot, and desktop API cancel flows now call session.mark_dirty() after appending denial entries instead of direct attribute assignment. Four sites updated across /cancel handlers and tool result update paths.
Prompt building workflow operations prompt_builder.py	Prompt construction functions (_compact_history, _inject_system_directive, _sync_basic_facts_into_system_prompt, _merge_memory_context_into_system_prompt, _normalize_single_system_message) now call session.mark_dirty() when modifying system prompt or message history. Six sites updated; all conditional logic for when to mark dirty remains unchanged.
Refactor documentation commit_message.txt	Commit message documents the switch from direct attribute assignment to the method call for alignment with session dataclass performance semantics.

🎯 2 (Simple) | ⏱️ ~8 minutes

A refactor most neat,
mark_dirty() calls so sweet,
No logic shall shift—
Just methods—a gift! 🐰✨

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 15.79% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and accurately summarizes the main change: replacing direct attribute assignments with a method call across the codebase.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

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• Commit unit tests in branch jules/refactor-history-dirty-7680221199825390300

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[Copilot]

Pull request overview

This PR refactors session mutation tracking by replacing direct session.history_dirty = True assignments with the encapsulated session.mark_dirty() call, aligning code usage with the Session dataclass’s documented performance semantics.

Changes:

• Replaced session.history_dirty = True with session.mark_dirty() across agent, CLI, bot, desktop bridge, and prompt-building flows.
• Ensured history mutations in prompt/system directive injection and compaction paths mark the session as dirty via the method.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
prompt_builder.py	Uses session.mark_dirty() after history/system-prompt mutations (compaction, directive injection, normalization, memory merge).
desktop/api_bridge.py	Uses session.mark_dirty() after cancel flow mutates tool/history state.
cli.py	Uses session.mark_dirty() after appending tool/user-facing messages in signal handler flows.
bot.py	Uses session.mark_dirty() after cancel flow appends denial message and clears pending confirmations.
agent.py	Uses session.mark_dirty() after appending user/tool/assistant messages and tool results.
commit_message.txt	Adds a commit-message artifact file (not referenced elsewhere).