Gemel

Evidence-native version control for agentic software development.

Gemel is a distributed version-control system built from first principles for agentic software engineering. Its native unit of version control is an evidence-bearing change: a durable record of what was attempted, against which exact state, by which producer, through which operations, with which claims, supported by which evidence, contradicted by which residuals, and resulting in which state.

Gemel is a machine-usable memory substrate for software engineering — a repository that answers not only what changed, when, by whom, but what was attempted, why, against what exact state, what the change claims, what evidence supports it, what contradicts it, what remains unexplained, which alternatives failed, and what the next agent should inspect.

Git stores surviving snapshots and ancestry. Gemel preserves intent, developmental trajectory, intermediate operations, provenance, agent execution identity, claims, evidence, residual disagreement, failed attempts, verification scope, reconciliation decisions, and exact reproducibility information — in a content-addressed, immutable, deterministically encoded object model implemented in native Rust.

Status

Phase 6 — Distributed Operation — complete. Next: Phase 7 (agent protocol / hosted workflows).

Phase 5 — Semantic Depth — complete.

Phase 4 — Git Interchange — complete. Phase 1.5 — Git-Carried Exchange Rollups — complete.

Phase 3 — Reconciliation — complete.

Phase 2 — Agent-Native Value — complete.

Phase 1 — Minimal Useful Gemel — complete.

Phase 0 — Specification before features — complete.

Seven normative documents (docs/): SPECIFICATION, OBJECT_MODEL, STORAGE, INVARIANTS, GIT_INTEROP, AGENT_PROTOCOL, THREAT_MODEL.
Canonical encoding (GCE): deterministic, fail-closed, extension-preserving binary grammar (the gemel crate, src/).
BLAKE3-256 object identity; twenty-four object families specified field-by-field.
Executable golden fixtures (golden/) pinning canonical bytes and identities, with a regeneration policy.

Phase 1 delivers the minimal useful system on a local, offline store:

gemel init — repository creation with canonical default producer + config.
gemel status — trajectory, intent, working-tree delta, claims, residuals, readiness.
gemel snapshot — record the working tree as a content-addressed state.
gemel change begin / change finish — the evidence-bearing change workflow: intent, operations, resulting state, basic claims/evidence/residuals, trajectory.
gemel log, show, diff (deterministic Myers), checkout, fsck.
Immutable, sharded, hash-verified object store with journaled atomic refs.
A disposable SQLite derived index (rebuildable; fsck detects drift).
Retention tiers and tombstones (GC pass is Phase 2+).
--json output on every command (gemel.query.v1 envelope).
The demonstration State S0 → Intent I1 → Trajectory T1 → Change C1 → State S1 with byte-exact content-addressed reconstruction, proven by tests/phase1_tests.rs.

Phase 2 delivers the agent-native query surface Git fundamentally lacks:

gemel why <subject> — causal blame: subject → Change → Intent → Claim → Evidence → Residual → previous approaches (rejected/interrupted trajectories preserved).
gemel claims / evidence / residuals — filtered, paginated, with derived statuses (never stored truth), dispositions, and freshness (MAY_REQUIRE_REFRESH).
gemel attempts <subject> — what was tried, why it ended, its evidence/residuals.
gemel trajectory <id> — the full materialized change sequence + handoff; trajectory close publishes a chained outcome (closed trajectories are terminal; new work on the same intent spawns a fresh attempt).
gemel checkpoint — a machine-generated continuation boundary (intent, trajectory, state, open claims, unresolved residuals, important evidence, continuation scope).
gemel context <subject> --budget N — the smallest sufficient context: phased, budget-bounded, deduplicated bundles with progressive-disclosure levels.
gemel residual resolve — chained disposition events (open/acknowledged/resolved/…).
The §52 acceptance demo — two agents, no shared conversation — proven by tests/phase2_tests.rs.

Phase 3 delivers reconciliation and concurrent workspaces:

gemel reconcile T1 T2 [--plan|--apply] — merges trajectories from a common base into a chosen direction: adopted / rejected / unresolved residuals / claims retained + invalidated / verification required / resulting State.
Per-path first-input-trajectory-wins adoption; textual conflicts with certainty: observed; claim interactions with certainty: possible — uncertainty is exposed, never invented.
gemel reconcile --plan — pure, deterministic, read-only (the resulting state identity is computed in memory, nothing is published).
Inputs are never erased: rejected changes and their claims/evidence/residuals stay canonical (negative knowledge, brief §7).
Named workspaces + --worktree (brief §34): change begin/finish --workspace wa --worktree /path/wa — concurrent agents never serialize merely to avoid filesystem collisions; proven by tests/phase3_tests.rs.

Phase 1.5 delivers Git-carried exchange rollups — Gemel's richer model travels through ordinary Git infrastructure without reducing Gemel to Git's ontology:

Immutable, content-addressed packs (GXPK, gemel.exchange.pack.v1) and Frontier Descriptors (gemel.exchange.frontier.v1) under .gemel/exchange/v1/ — append-only publication (packs first, frontier last), deterministic partitioning (256 KiB target), no timestamps/hostnames/git-commit-ids in descriptors.
A narrowly scoped .gemel/.gitignore keeps the native store invisible to Git while the exchange namespace is tracked (git status stays clean).
Quarantine ingestion: every artifact is hostile input — identity verification, schema checks, resource limits, bounded parent chains, no execution, idempotent; conflicts (same id, different bytes) are fatal (§42).
Source-state binding: the frontier's source_state is the pure-content State of the checked-out tree; a Git-only source change flips the context to CONTEXT_STALE / SOURCE_CONTEXT_DIVERGED instead of pretending old evidence verifies new source.
Zero-ceremony bootstrap: git clone && gemel status --json restores the engineering frontier (trajectory, intent, claims, residuals, readiness) with no gemel init, no server, no manual import; imported names (T1/C1/S1) continue the local counters.
gemel exchange status|export|ingest|verify (frontier/portable profiles, --working-tree/--git-index verification for CI), auto-export on change finish inside Git worktrees, and gemel fsck reporting native_store + exchange_transport sections with exchange-omitted warnings distinct from corruption.
33 integration courts with real Git repositories: transport, shallow clone, branch-merge unions, Git-only mutation, corruption classes, idempotence, byte determinism across paths, non-interference, git cleanliness, index independence, incremental export, golden fixtures — tests/exchange_tests.rs.
Normative exchange protocol: docs/EXCHANGE.md (a second implementation must be possible from the specification alone).

Phase 4 delivers deterministic Git interchange (GIT_INTEROP.md):

gemel export-git — projects the head's causal-parent closure into ordinary Git commits (loose objects via the pure-Rust git_io), with GEMEL-CHANGE/INTENT/ TRAJECTORY/CLAIM/EXPORT-VERSION trailers, deterministic authors/timestamps (no wall clock), and canonical mapping objects under refs/mappings/export/.
gemel import-git — topological import of real Git histories (packed or loose): states from Git trees, deterministic operations with conservative rename detection, first-parent-chain trajectories, synthetic git_import/human/ unknown producers, refs/mappings/import/ with trailer re-linking, hostile trailer rejection, and idempotent re-import. Provenance Git cannot supply is unknown, never fabricated.
gemel clone <url> — git clone + native store + import in one step.
The provable round-trip core: trees/topology/messages/authors/timestamps survive Git→Gemel→Git exactly; identity linkage survives Gemel→Git→Gemel through trailers (re-import into the originating repository re-links the original objects).
9 courts in tests/git_interop_tests.rs using real Git repositories.

Phase 5 delivers language-aware semantic depth (OBJECT_MODEL.md §6.23–§6.24; brief §22–§24, §13):

Two new canonical families — semantic-entity and semantic-index — published by gemel index (deterministic; unchanged entities deduplicate by content identity).
A deterministic lexical Rust extractor (src/semantic/rust.rs): strings, raw strings, char literals, line/nested-block comments, attributes, lifetimes, generics; pub fn/struct/enum/union/trait/impl Trait for Type/mod (inline + file)/const/static/use/macro_rules/extern "C" fn/type aliases; nested inline modules.
Explicit lineage, never inferred identity: edited entities link lineage_from with certainty observed (same-name-kind-path); moved entities link with certainty possible (similarity:same-name-kind) and a documented evidence string. Semantic identity survives file movement without silent merges.
gemel semantic <subject> — resolve entities by name, path::name, file:line, or identity; gemel diff --semantic — added/removed/modified/moved entities with body-digest detection of edits; gemel why/attempts — resolve semantic subjects and match across lineage aliases so moved entities surface the work that touched their ancestors.
The indexer producer is published, fsck stays clean, and the exchange frontier carries the semantic graph: a depth-1 git clone + gemel status --json re-establishes refs/semantic/* over the imported objects with identical identities (12 courts in tests/phase5_tests.rs).

Phase 6 delivers native distributed operation (DISTRIBUTED.md; STORAGE.md §10):

gemel remote add|remove|list, gemel fetch|push|pull — transport-agnostic sync: content-identity negotiation (reachable_ids/missing_ids), verified gemlpack transfers, and atomic validated ref publication. A re-push transfers nothing; resumed fetches re-negotiate from the new have-set.
Public-ref policy: only knowledge refs travel (head, names, trajectories, semantic indexes, …); workspace, exchange-marker, and mapping bookkeeping never leaves home. Fetched refs track under refs/remotes/<name>/*.
Fail-closed integrity: every envelope is re-verified end-to-end; a corrupt remote aborts with local state untouched; same-id different-bytes is fatal; a diverged pull refuses and preserves local work for gemel reconcile.
Git-only remotes receive the deterministic export/import projections.
10 courts in tests/phase6_tests.rs (identical identities across machines, negotiation dedup, multi-producer + semantic transport, corruption, conflict, divergence, Git projection, fsck-clean sync).

Reading order

docs/SPECIFICATION.md — purpose, principles, architecture, conformance matrices.
docs/OBJECT_MODEL.md — the ontology: encoding, identity, all object families.
docs/STORAGE.md — persistence, refs, indexes, retention, fsck.
docs/INVARIANTS.md — the complete correctness contract.
docs/GIT_INTEROP.md — deterministic Git interchange.
docs/AGENT_PROTOCOL.md — the machine query surface.
docs/DISTRIBUTED.md — native sync protocol (Phase 6).
docs/EXCHANGE.md — Git-carried exchange rollups (Phase 1.5).
docs/THREAT_MODEL.md — security model and fail-closed catalog.

Layout

src/                    the single `gemel` crate
├── lib.rs              crate root
├── primitive layer     varint, family table, Gid, hex, limits, value model
├── encoding layer      spec tables, encode/decode, hashing, validation, JSON projection
├── store/              object store, refs+journal, lock, index, tombstone, retention, fsck
├── content.rs          working tree ↔ state, tree deltas, operation synthesis, Myers diff
├── workflow.rs         change begin/finish, intents, trajectories, checkpoint,
│                       trajectory close, residual resolve
├── semantic/          Phase 5: deterministic Rust extractor, entity/index objects,
│                      lineage, semantic diff/resolution
├── sync/              Phase 6: gemlpack transfer format, transport trait,
│                      negotiation, fetch/push/pull, remotes config
├── query.rs           log/show/status, why/claims/evidence/residuals/attempts/
│                      trajectory/context bundles, derived statuses, pagination
├── exchange/           Phase 1.5: pack/frontier encoding, deterministic export,
│                       quarantine ingest, source-state binding (EXCHANGE.md)
├── git_adapter.rs      isolated `git` index/staged-tree adapter (argv-safe)
├── git_io.rs           pure-Rust loose-object/tree/commit read-write (Phase 4 base)
├── ignore.rs           .gitignore matcher (documented subset of git semantics)
├── defaults.rs         default producer/config/retention builders
├── golden/             executable golden fixture definitions
└── bin/
    ├── gemel.rs        the CLI (init status snapshot change log show diff checkout fsck
    │                   why claims evidence residuals attempts trajectory checkpoint
    │                   context reconcile exchange)
    └── golden-gen.rs   golden vector generator
golden/                 pinned golden vectors (canonical bytes + identities)
docs/                   the normative specification set
tests/                  Phase 1 + 2 + 3 + 1.5 + 4 + 5 + 6 integration suites (the acceptance demos)

Layering is disciplined within the crate: primitives → encoding → schema → fixtures → store → workflow/query → CLI; nothing depends upward.

Validation

cargo test                       # unit + golden + Phase 1/2/3/1.5 integration suites
cargo clippy --all-targets       # zero warnings
cargo run --bin golden-gen       # golden vectors up to date (protocol-change only)

Golden vectors must never be regenerated casually: any change to a pinned digest is a breaking protocol change (docs/OBJECT_MODEL.md §10.4).

Quick demo