A two-agent ablation study on whether repository context files (AGENTS.md / CLAUDE.md) change how well LLM coding agents solve real GitHub issues.

This is the code-and-data release for the paper "Do Context Files Help Coding Agents? A Two-Agent Ablation Study on Real Repositories" (REALM @ EMNLP 2026, under review). It contains the full experimental harness, the safety infrastructure, the benchmark task specifications, the statistical analysis scripts, and an aggregated per-cell results table.

We run two production coding agents (Claude Code and OpenAI Codex CLI) on real, merged pull-request tasks from three Python repositories, under three context-injection strategies, and measure whether the presence of a repository context file changes task correctness and efficiency.

Headline finding — a correctness null, replicated across both agents. Adding the repository's AGENTS.md (in full, or via a retrieval-style split) does not measurably change the probability that the agent's patch passes the gold PR tests.

• Within-task omnibus permutation test: p = 1.000 (Claude); no detectable effect on either agent.
• TOST equivalence: effect bounded to ≤10pp (Claude) / ≤15pp (Codex).
• The result is power-limited, and we say so: at n≈15–17 tasks × 3 repeats the minimum detectable effect is >30pp; detecting a 10pp effect at 80% power would need ~120 tasks. We report this as the binding constraint, not a proof of zero.

Where context did move the needle — process efficiency, not outcome. On the OpShin/opshin tasks, Claude Code with context ran the slow full test suite far less often (blind full-suite runs 3.67 → 2.44 → 1.67 across none→always_on→selective), cutting wall-clock time ~24% — because the AGENTS.md warns the suite is slow and nudges the agent toward targeted tests. The takeaway is process, not pass-rate.

Manipulation-validity probe. A targeted probe confirms the injection channel is live (the agent reads and rates the file as useful) yet does not flip skill-gated tasks upward — context can narrowly depress correctness but never manufactured a pass.

• Independent variable — context-injection strategy:
  • none — strip AGENTS.md/CLAUDE.md from the workspace; no system-prompt context.
  • always_on — inject the full context file into the system prompt.
  • selective — split the file into a wiki and give the agent a retrieval hint.
• Dependent variables
  • Correctness — binary, via a SWE-bench-style Tier-C eval: run the gold PR tests against the agent's patch; pass iff all gold tests pass with zero failures/errors.
  • Efficiency — portable cross-agent metrics: tool calls, wall-clock duration, output tokens. (Turn counts and prompt-cache tokens are agent-specific and are not compared across agents.)
• Design — within-task paired, n=3 repeats per cell; unit of analysis = task.
• Repositories — OpShin/opshin, firebase/firebase-admin-python, pdm-project/pdm.
• Statistics — Wilson CIs, task-clustered bootstrap (10k), sign-flip permutation, within-task omnibus permutation, TOST equivalence, Monte-Carlo power.

harness/                 # the experiment engine
  agent.py               #   ClaudeCodeAgent + CodexCLIAgent (stream parsing, watchdog)
  runner.py              #   per-cell orchestration, strategy application, history pruning
  config.py              #   run configuration / knobs
  context.py             #   strategy injection: none / always_on / selective
  generate_wiki.py       #   builds the retrieval wiki for the `selective` strategy
  evaluate.py            #   Tier-C gold-test evaluation pipeline
  tools.py, db.py, logger.py
  task_generator*.py     #   build benchmark tasks from merged PRs
pod/                     # cloud-pod bring-up + DEFENSE-IN-DEPTH safety layer
                         #   egress lock, push-deny hooks, verify_lock gate
tasks/                   # benchmark task specifications (JSON)
data/
  results_summary.csv    # aggregated per-cell outcomes (no raw transcripts)
  experiment_full.db     # raw per-run/per-turn data, 291-run ablation
  probe_codex.db, probe_claude.db   # raw data, 36-cell probe
  README.md              #   column dictionary + reproduce snippet
paper/                   # data/key_numbers.md — provenance for every number in the paper
analyze.py, power_analysis.py, efficiency_analysis.py, ...   # analysis scripts
AGENTS.md                # OpShin's own context file — the artifact injected under
                         #   `always_on`/`selective` for the OpShin task set

Not included here (heavy or sensitive, available from the authors on request): cloned target repositories, raw agent transcripts (*.jsonl), and external datasets. experiment_full.db, probe_codex.db, and probe_claude.db (generated diffs, per-run/per-turn metrics) are released in data/. See .gitignore.

Coding agents execute shell commands. To keep a misbehaving agent from touching external state (pushing code, opening PRs, leaking the gold answer), the harness uses defense-in-depth (see pod/ and paper Appendix A):

1. DNS blackhole for GitHub (egress lock).
2. git remote remove on every workspace remote.
3. git push / commit / remote / gh denied via PATH shims and the agent's own deny-hooks (--disallowedTools for Claude; a PreToolUse deny hook for Codex).
4. GH_TOKEN / GITHUB_TOKEN stripped from the environment.
5. Future git history pruned so the agent cannot read the gold commit.
6. A hard verify_lock gate that refuses to run unless all of the above hold.

pip install -r requirements.txt

# correctness marginals + efficiency straight from the shipped CSV
python3 - <<'PY'
import pandas as pd
df = pd.read_csv("data/results_summary.csv")
print(df.groupby(["agent","strategy"]).task_passed.mean().mul(100).round(1))
PY

# full statistical analysis
python3 power_analysis.py data/experiment_full.db claude_code
python3 power_analysis.py data/experiment_full.db codex
python3 efficiency_stats_correct.py

The paper itself is on arXiv — https://arxiv.org/abs/2607.27250 (see paper/README.md), not duplicated in this repo.

Paper under review at REALM @ EMNLP 2026; also posted as an arXiv preprint: https://arxiv.org/abs/2607.27250.

@misc{khatri2026contextfiles,
  title  = {Do Context Files Help Coding Agents? A Two-Agent Ablation Study on Real Repositories},
  author = {Khatri, Prakhar},
  year   = {2026},
  eprint = {2607.27250},
  archivePrefix = {arXiv},
  primaryClass  = {cs.SE},
  url    = {https://arxiv.org/abs/2607.27250}
}

Code released under the MIT License. The aggregated results data in data/ is provided for research use under the same terms.