Developer reference · protected main 805f3d6
Follow authority through the whole system
These guides explain who owns each record, what enters and leaves the boundary, which invariants fail closed, and where application convenience stops. Closely related projects are grouped when they implement one developer concept.
Read the repository by responsibility
Dependency rule: domain and scientific-record projects own meaning. Application services, CLI, desktop, renderers, providers, plugins, and model clients may depend inward, but Core never reaches outward to them.
No module guide matches that filter.
Foundation
Identity, protocol, and executable workflow semantics
Stable values and accepted conduct definitions come before any product surface.
FoundationImplemented
Kernel
Canonical identifiers, digest-bound values, deterministic validation, and fail-closed primitives used across the system.
Kernel guideFoundationImplemented
Shared
Narrow cross-module value types that preserve domain isolation without becoming a miscellaneous dependency bucket.
Shared guideProtocolImplemented
Protocol
Drafts, approvals, immutable versions, amendments, supersession, and the authority that binds research conduct.
Protocol guideGraphImplemented
Workflow
Template and graph compilation: nodes, dependencies, gates, deterministic plans, and invalidation relationships.
Workflow guideState machineFE-03
Workflow Execution
Append-only transitions and deterministic replay over a compiled workflow. This is the state-machine half of the workflow model.
Workflow Execution guideEvidence and history
Immutable bytes, snapshots, provenance, and portable verification
These modules make state independently identifiable and history reconstructable.
EvidenceImplemented
Artifacts
Raw-byte identity, immutable artifact references, digest domains, and verification before trust.
Artifacts guideHistoryImplemented
Provenance
Append-only activities, actors, evidence references, lineage, and reconstruction points for scientific mutations.
Provenance guidePortabilityFE-06
Bundles
Manifest-bound packages, verification findings, and Bundle v2 transport without transferring scientific authority.
Bundles guideAuthorityFE-01
Corpus Snapshots
Immutable candidate-set identity, lineage, successor publication, and equality rules shared by decision workflows.
Corpus Snapshots guideReview conduct
From imported observations to governed review outputs
Each stage cites earlier evidence and adds bounded decisions; it does not rewrite the input history.
AcquisitionImplemented local import
Search
Search plans, source files, parsed records, warnings, stable identities, and reproducible import traces.
Search guideReviewFE-02
Deduplication
Evidence graphs, exact and fuzzy candidates, human merge decisions, corrections, and successor snapshots.
Deduplication guideHuman authorityFE-04
Screening
Independent title/abstract decisions, criteria binding, conflicts, adjudication, invalidation, and replay.
Screening guideLocal evidenceFE-05
Full Text
No-network intake, exact PDF bytes, derived extraction evidence, decisions, corrections, and verification.
Full Text guideOutputsFE-06
Reporting
Conserved counts, deterministic reports, Rapid Review governance, export ledger, and persisted verification.
Reporting guideEvidence analysis
Structured claims without synthesis overreach
FE-07 keeps extracted data, quality judgments, and synthesis planning separate and evidence-bound.
FE-07Implemented
Extraction
Schema-bound fields, exact evidence locations, author and correction lineage, and amendment invalidation.
Extraction guideFE-07Implemented
Appraisal
Instrument-bound quality judgments whose evidence, actor, scope, and corrections remain explicit.
Appraisal guideFE-07Plan-only
Synthesis
Deterministic synthesis plans and eligibility bindings without claiming that statistical analysis has run.
Synthesis guideApplication and product
Durable local workspaces and authority-checked entry points
These projects orchestrate Core behavior. They do not acquire independent scientific authority.
PersistenceLocal files
Research Workspace
Transactional local generations, manifests, verification, recovery, atomic promotion, and durable command results.
Research Workspace guideCompositionApplication layer
AppServices
Read projections and command-facing composition over admitted domain contracts.
AppServices guideDesktopAuthority adapter
Desktop AppServices
Preview, confirmation, expected-state bindings, readiness checks, and fail-closed product command routing.
Desktop AppServices guideProduct hostFE-08
Desktop
Avalonia product shell, workspace opening, safe local operations, and visible authority-state handling.
Desktop guideOperator surfaceImplemented
CLI
Local initialization, import, verification, decisions, replay, reporting, bundle, and export commands.
CLI guideUI contracts and adapters
Portable presentation without UI-owned science
Renderers communicate intent and state; authority remains in accepted Core and application contracts.
Renderer-neutralImplemented
UiContracts
Workspace plans, research blocks, status, actions, and renderer-independent presentation contracts.
UiContracts guideAvaloniaRenderer
Avalonia Blocks
Reusable block rendering and sample-host behavior outside the Core dependency boundary.
Avalonia Blocks guideIntegrationBoundary guide
Bridges
How application, UI, provider, plugin, and future infrastructure adapters translate without smuggling authority inward.
Bridges guideExtensions and governed assistance
Capabilities, staged output, and proposals
The current contracts define safe boundaries. FE-10 and FE-11 still require their own accepted gates before runtime claims are valid.
Contracts implementedFE-10 runtime planned
Extensibility and plugin runtime
Manifest identity, scoped capabilities, invocation envelopes, staged output, validation, and the difference between isolation and a security sandbox.
Extensibility guideContracts implementedFE-11 governance planned
AI
Evidence-bound task and proposal contracts, privacy declarations, schema validation, and explicit human acceptance.
AI guideDo not infer maturity from a namespace
A project in src/ can be a stable local contract, a supporting application layer, an experimental renderer, or a boundary prepared for later work. Read the status and non-claims in its guide, then follow the linked ADR, gate, source, and tests.