Agent Context System#

The Problem#

Agents start from zero every session. You spend an hour getting your coding agent up to speed on a project, close the session, and start from zero the next day. The agent forgot everything. Every session is a cold start.

This isn't a limitation of the model. It's a context delivery problem. The agents have the capacity to remember — they just don't have the right inputs at the right time in the right format.

The Solution#

Two markdown files. One committed, one gitignored. The agent reads both at the start of every session and updates the local one at the end.

• AGENTS.md — Your project's source of truth. Committed and shared. Always in the agent's prompt. Under 120 lines. Contains compressed project knowledge: patterns, boundaries, gotchas, commands, architecture.

• .agents.local.md — Your personal scratchpad. Gitignored. Grows over time as the agent logs what it learns each session. Session notes, dead ends, preferences, patterns that haven't been promoted yet.

That's it. No plugins, no infrastructure, no background processes. The convention lives inside the files themselves, and the agent follows it.

How It Works#

1. Setup#

Run the init script. It creates .agents.local.md from a template, ensures it's gitignored, and wires up your agent tool's config (CLAUDE.md symlink for Claude Code, .cursorrules for Cursor, .windsurfrules for Windsurf, copilot-instructions.md for Copilot).

bash

# If you cloned the template repo:
./scripts/init-agent-context.sh

# If you installed as a skill (npx skills add):
bash .agents/skills/agent-context-system/scripts/init-agent-context.sh

Then edit AGENTS.md with your project specifics: name, stack, commands, actual patterns and gotchas from your codebase. This is the highest-leverage edit you'll make.

2. During Sessions#

The agent reads both files at session start. AGENTS.md gives it compressed project knowledge. .agents.local.md gives it accumulated learnings from past sessions. The agent now has context that persists across sessions.

At session end, the agent appends to the scratchpad's Session Log: what changed, what worked, what didn't, decisions made, patterns learned. Most agents (Copilot Chat, Cursor, Windsurf) don't have session-end hooks, so this depends on Rule 7 in AGENTS.md being seen and acted on, or the user saying "log this session." Claude Code handles this automatically via auto memory.

3. Over Time#

The scratchpad grows. When it hits 300 lines, the agent compresses: deduplicate, merge related entries, keep it tight. During compression, if a pattern has shown up across 3+ sessions, the agent flags it in the scratchpad's "Ready to Promote" section using the same pipe-delimited format that AGENTS.md expects.

You decide when to move flagged items from the scratchpad into AGENTS.md. The scratchpad is where things are experimental. AGENTS.md is where proven knowledge lives.

text

Session notes → .agents.local.md → agent flags stable patterns → you promote to AGENTS.md
                    (personal)                                        (shared)

Scripts#

The template includes five scripts:

init-agent-context.sh#

Sets up the local agent scratchpad and agent tool integrations. Run once per clone. Safe to re-run.

• Creates .agents.local.md from template
• Ensures .agents.local.md is gitignored
• Asks which agents you use (Claude, Cursor, Windsurf, Copilot) and wires up the right config
• Creates CLAUDE.md symlink for Claude Code (since it doesn't read AGENTS.md yet)
• Adds agent context directive to .cursorrules, .windsurfrules, or copilot-instructions.md

compress.sh#

Compresses the scratchpad when it exceeds 300 lines. Deduplicates, merges related entries, flags stable patterns for promotion. Not yet implemented — instructions for the agent are in AGENTS.md's Local Context section.

promote.sh#

Moves flagged items from .agents.local.md's "Ready to Promote" section into AGENTS.md. Not yet implemented — currently a manual step.

validate.sh#

Validates AGENTS.md stays under 120 lines and checks format consistency. Not yet implemented.

publish-template.sh#

Push to GitHub and mark as a template repo. Run once. Creates a private GitHub repo and marks it as a template so you can use it to create new projects with gh repo create my-project --template YOUR_USERNAME/agent-context-system --private.

Knowledge Flow#

Knowledge doesn't just sit in one place. It flows.

Learnings start as session notes in .agents.local.md. The agent writes them at the end of each session. During compression, if a pattern has shown up across 3+ sessions, the agent flags it in the scratchpad's "Ready to Promote" section using the same pipe-delimited format that AGENTS.md expects. Then you decide when to move it into AGENTS.md.

text

Session notes → .agents.local.md → agent flags stable patterns → you promote to AGENTS.md
                    (personal)                                        (shared)

The scratchpad is where things are still experimental. AGENTS.md is where proven knowledge lives. The agent flags candidates. You make the call.

AGENTS.md Template Structure#

The template AGENTS.md includes:

Project#

Basic metadata: name, stack, package manager. Keep it one-liners.

Commands#

Executable commands for build, test, lint, dev server. These go early because agents need them immediately.

Architecture#

One line per directory. The agent gets high-level structure on every turn without needing to look anything up.

Project Knowledge (Compressed)#

This is the most important section. Three subsections:

• Patterns — pattern | where-to-see-it format. Named exports only, server components default, Zustand for client state, Result types not try/catch.
• Boundaries — rule | reason format. Never modify src/generated, env vars through src/config, no default exports, no inline styles.
• Gotchas — trap | fix format. pnpm build hides type errors, dev sessions expire after 24h, integration tests need DB up.

Vercel's evals showed passive context (always in the prompt) achieves 100% pass rate vs 53% when agents must decide to look things up. This section is passive context. The agent gets it on every turn automatically.

Rules#

Numbered list. Read AGENTS.md and .agents.local.md first. Plan before code. Locate files before changing. Only touch what the task requires. Run tests after every change. Summarize changes.

Deep References#

Points to agent_docs/ for when a task needs more depth than the compressed version provides. Conventions, architecture, gotchas — full detail, loaded on demand.

Local Context#

Instructions for reading and updating .agents.local.md. Explains session-to-session learning, compression protocol, promotion pathway. Tells subagents to explicitly read the scratchpad (they don't inherit main conversation history).

.agents.local.md Template Structure#

The template .agents.local.md includes:

Preferences#

Your style, code preferences, planning preferences. Friendly vs technical tone. Minimal changes vs comprehensive refactors. Always state the plan before writing code.

Patterns#

Settled truths about this project. Promote recurring session learnings here.

Gotchas#

Things that look right but aren't. Include WHY.

Dead Ends#

Approaches tried and failed. Include WHY they failed. Saves the agent from repeating mistakes.

Ready to Promote#

The agent flags items here during compression when a pattern has recurred across 3+ sessions. Use the same pipe-delimited format AGENTS.md expects. The human decides when to move flagged items into AGENTS.md.

Session Log#

Append new entries at the END. One entry per session. Keep each to 5-10 lines. Template: what changed, what worked, what didn't, decisions, learnings.

Compression Log#

When the file exceeds 300 lines, compress. Log it here.

Agent Compatibility#

The template works across all major agent tools:

AgentConfig FileWhat It DoesClaude CodeCLAUDE.mdSymlink → AGENTS.md (Claude doesn't read AGENTS.md yet)Cursor.cursorrulesDirective pointing to AGENTS.mdWindsurf.windsurfrulesDirective pointing to AGENTS.mdGitHub Copilot.github/copilot-instructions.mdDirective pointing to AGENTS.md

Claude Code Auto Memory#

Claude Code shipped auto memory in late 2025. It creates a ~/.claude/projects/<project>/memory/ directory where Claude writes its own notes and loads them at session start. That's basically the .agents.local.md concept built into the tool.

If you use Claude Code exclusively, auto memory handles session-to-session learning and the scratchpad is optional. The template's value for you is the AGENTS.md file itself and the promotion pathway that gives you a structured way to take what auto memory learns and move the stable parts into your root file.

If your team uses multiple agents (GitHub just shipped Agent HQ with Copilot, Claude, and Codex side by side), the scratchpad matters because auto memory only works in Claude Code. The scratchpad works everywhere.

Subagent Context#

Claude Code now ships subagents. Copilot CLI just shipped /fleet in experimental mode. Both tools are moving toward the same model: a lead agent that coordinates a team of specialists.

Subagents don't inherit the main conversation's history. Each one starts with a clean context window. The only shared knowledge they all have is your root instruction file.

So when you go from one agent to five parallel agents, AGENTS.md goes from "helpful project context" to "the only thing preventing five agents from independently making conflicting decisions about your codebase."

The compressed project knowledge, the boundaries section, the gotchas — that's the shared brain. Without it, each subagent rediscovers your project from scratch.

This is why the template explicitly tells subagents to read .agents.local.md too. They won't get it by default. They need the instruction.

It's also why instruction budget discipline matters even more. If your AGENTS.md is 500 lines, you're paying that token cost for every subagent you spawn. Under 120 lines is a feature, not a limitation.

Research Foundation#

This template is built on research from:

• LangChain — Context Engineering for Agents: Write/Select/Compress/Isolate framework
• HumanLayer — Writing a Good CLAUDE.md: instruction budgets, root file discipline
• GitHub — Lessons from 2,500+ Repositories: what makes agents.md files actually work
• Vercel — AGENTS.md Outperforms Skills: passive context vs skill retrieval eval data
• Anthropic — Equipping Agents with Skills: three-tier progressive disclosure
• AI Hero — A Complete Guide to AGENTS.md: cross-platform standard adoption
• Anthropic — Claude Code Subagents: context isolation, custom agents
• GitHub — Copilot CLI /fleet: parallel fleets with dependency-aware tasks

Key finding: frontier LLMs reliably follow about 150-200 instructions. Claude Code's system prompt already uses about 50. So anything in your root file that isn't universally applicable risks getting quietly deprioritized.

That's why AGENTS.md stays under 120 lines and uses compressed formats (pipe-delimited patterns, boundaries, gotchas). Dense beats verbose.

Another key finding: Vercel's evals showed passive context (always in prompt) achieves 100% pass rate vs 53% when agents must decide to look things up. Available docs aren't the same as used docs. Put critical knowledge where the agent literally cannot miss it.

Getting Started#

New repo from template#

bash

gh repo create my-project --template YOUR_USERNAME/agent-context-system --private
cd my-project
chmod +x scripts/init-agent-context.sh
./scripts/init-agent-context.sh

Installed as a skill#

If you installed via npx skills add, the scripts live inside the skill directory, not at the project root. Run from there:

bash

bash .agents/skills/agent-context-system/scripts/init-agent-context.sh

Existing repo#

Copy AGENTS.md, agent_docs/, and scripts/ into your project root, then run the init script.

Publish this as your template#

bash

chmod +x scripts/publish-template.sh
./scripts/publish-template.sh

After Setup#

1. Edit AGENTS.md. Fill in your project name, stack, commands. Replace the placeholder patterns and gotchas with real ones from your codebase. This is the highest-leverage edit you'll make.
2. Fill in agent_docs/. Add deeper references. Delete what doesn't apply.
3. Customize .agents.local.md. Add your preferences.
4. Work. The agent reads everything, does the task, updates the scratchpad.
5. Promote what sticks. During compression, the agent flags patterns that have recurred across 3+ sessions in the scratchpad's "Ready to Promote" section. You decide when to move them into AGENTS.md.

File Structure#

text

your-repo/
├── AGENTS.md                    # Committed. Always loaded. Under 120 lines.
├── .agents.local.md             # Gitignored. Personal scratchpad.
├── agent_docs/                  # Deeper docs. Read only when needed.
│   ├── conventions.md           # Full code patterns, naming, file structure
│   ├── architecture.md          # System design, data flow, key decisions
│   └── gotchas.md               # Extended known traps with full explanations
├── scripts/
│   ├── init-agent-context.sh    # Setup script (run once per clone)
│   ├── publish-template.sh      # Publish as GitHub template repo
│   └── agents-local-template.md # Template for .agents.local.md
└── CLAUDE.md                    # Symlink → AGENTS.md (created by init)

License#

MIT