- Added branch-aware session loading so autoresearch state only rehydrates for current branch.
- Replaced user-specified experiment commands with fixed `bash autoresearch.sh` execution flow.
- Enforced safer setup checks, including missing `autoresearch.sh` and uncommitted-worktree errors.
- Added branch-specific storage helpers, baseline-commit persistence, and expanded tests for dirty-path cases.
- Replaced file-backed autoresearch contracts with sqlite-backed session/run storage in `~/.omp/autoresearch`.
- Added `AutoresearchStorage` and rewired `init_experiment`, `run_experiment`, and `log_experiment` to persist sessions and runs.
- Added `update_notes` tool with `body`/`append_idea` inputs and updated prompts to use active-session context.
- Removed `autoresearch.md` contract parsing and checks flow, including `runChecks`, `force`, and timeout schema options.
- Updated autoresearch state/types to persist `goal`, `notes`, `branch`, and `baselineCommit` plus run justification/flag metadata.
- Added `new_segment` parameter to `init_experiment` to force new segment creation when contract fields match.
- Added `skip_restore` parameter to `log_experiment` to preserve working tree state and pre-existing uncommitted changes.
- Changed `log_experiment` to revert only run-modified files instead of entire working tree, preserving user changes.
- Changed `init_experiment` to detect matching contract fields and skip re-initialization unless `new_segment=true`.
- Added git status parsing utilities to track pre-run dirty paths and distinguish tracked vs untracked modifications.
- Removed secondary metrics validation requirement, making secondary metrics informational only.
- Extracted git operations from ControlledGit class into centralized utils/git module with 1276 lines of typed command wrappers.
- Replaced dependency injection of ControlledGit instances with direct cwd string parameters across commit agent tools and workflows.
- Migrated all git command execution from inline shell calls and custom helpers to structured git module API (diff, status, branch, worktree, patch, etc.).
- Removed ControlledGit class, operations.ts, and helper functions (findGitHeadPath, mergeStdoutStderr, joinPatch) now provided by git module.
- Exported git utilities from main package entry point for extension and plugin use.
- Added contract system for validating benchmark commands, metrics, scope paths, constraints, and off-limits paths.
- Contract validation enforces matching initialization parameters against autoresearch.md before init_experiment.
- Segment fingerprinting detects configuration drift and warns when metrics are not directly comparable.
- Added pending run detection and recovery to resume incomplete experiments from .autoresearch/runs/.
- Run directories organize artifacts with benchmark logs and optional checks logs for traceability.
- Extended experiment state to track run number, command, scope, off-limits, constraints, and fingerprint.
- Added git branch isolation for autoresearch sessions with automatic branch creation, reuse, and worktree safety checks.
- Added scope definition sections (Files in Scope, Off Limits, Constraints) to autoresearch template for explicit session boundaries.
- Added keybinding matcher utilities for consistent escape/cancel key handling across interactive components.
- Added ASI metadata validation (hypothesis and rollback context) in log_experiment tool for experiment tracking.
- Refactored keybinding logic across 13 components to use centralized matcher functions instead of inline key checks.
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