Long documents pose many challenges to current intelligent writing systems. These include maintaining consistency across sections, sustaining efficient planning and writing as documents become more complex, and effectively providing and integrating AI assistance to the user. Existing AI co-writing tools offer either inline suggestions or limited structured planning, but rarely support the entire writing process that begins with high-level ideas and ends with polished prose, in which many layers of planning and outlining are needed. Here, we introduce TreeWriter, a hierarchical writing system that represents documents as trees and integrates contextual AI support. TreeWriter allows authors to create, save, and refine document outlines at multiple levels, facilitating drafting, understanding, and iterative editing of long documents. A built-in AI agent can dynamically load relevant content, navigate the document hierarchy, and provide context-aware editing suggestions. A within-subject study (N=12) comparing TreeWriter with Google Docs + Gemini on long-document editing and creative writing tasks shows that TreeWriter improves idea exploration/development, AI helpfulness, and perceived authorial control. A two-month field deployment (N=8) further demonstrated that hierarchical organization supports collaborative writing. Our findings highlight the potential of hierarchical, tree-structured editors with integrated AI support and provide design guidelines for future AI-assisted writing tools that balance automation with user agency.