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Reading Guide

The aDNA Universal Standard is 1,336 lines. You don’t need all of them. This guide maps three reading paths by what you’re trying to do, provides a section-by-section table of contents, and disambiguates the skill/lattice dual identity.


1. Reading Paths

Three personas, three curated paths through the standard:

PersonaGoalSections to read~LinesTime
New adopterGet a working vault§1 (Intro), §2 (Terms), §3 (Triad), §4 (Governance), §5 (Directory Structure), §7 (Frontmatter)~35010-15 min
Extension builderAdd entity types, templates, pipelinesNew adopter path + §6 (Naming), §12 (Templates), §14 (Pipelines), §19 (Extensions)~55020-25 min
Standard contributorUnderstand the full specEverything1,33645-60 min

New Adopter Path

Read these six sections in order. They give you the structural foundation to set up and operate an aDNA vault.

  1. §1 Introduction & Scope — What aDNA is, who it’s for, RFC 2119 keywords
  2. §2 Terminology — 12 key terms (triad, governance file, bare/embedded, session, SITREP)
  3. §3 Triad Architecture — The who/what/how ontology, bare vs. embedded deployment forms
  4. §4 Governance Files — CLAUDE.md, MANIFEST.md, STATE.md, AGENTS.md, README.md — what each does
  5. §5 Directory Structure — Required/recommended/optional subdirectories for each triad leg
  6. §7 Frontmatter System — Required YAML fields, tag conventions, type-specific extensions

After this path: You can create and operate a standard aDNA vault. Come back for sessions (§8), missions (§9), and collision prevention (§13) when you need them.

Extension Builder Path

Start with the new adopter path above, then add these four sections:

  1. §6 Naming Conventionstype_descriptive_name.md pattern, ALLCAPS governance list, directory naming
  2. §12 Template System — Starter/Standard/Full template sets, template conventions
  3. §14 Content-as-Code Pipelines — Folder-based workflows where file location = processing state
  4. §19 Optional Extensions — Machine registry, backlog, skill files, testing/CI, reference code, ADRs

After this path: You can extend an aDNA vault with custom entity types, templates, pipelines, and optional subsystems.

Standard Contributor Path

Read everything. The appendices (§20) contain the persona framework, aggregation point patterns, deferred topics, and the full decision traceability matrix mapping all 40 design decisions to their spec locations.


2. Section Map

All 20 numbered sections of the standard with one-line summaries, persona tags, and line ranges.

§SectionSummaryPersonasLines
1Introduction & ScopeWhat aDNA is, who it’s for, RFC 2119 keywordsAll19-52
2Terminology12 key terms: triad, governance file, bare/embedded, session, SITREP, content-as-codeAll54-73
3Triad Architecturewho/what/how ontology, bare vs. embedded deployment forms, classification question testAll75-171
4Governance FilesFive ALLCAPS files (CLAUDE, MANIFEST, STATE, AGENTS, README) — purpose, contents, quickstartAll173-294
5Directory StructureRequired/recommended/optional subdirectories for each triad leg, starter/standard/full skeletonsAll296-462
6Naming ConventionsUnderscores not hyphens, type_descriptive_name.md, ALLCAPS governance list, type_ prefixesExtension+464-516
7Frontmatter SystemRequired base fields (type, created, updated, last_edited_by, tags), tag conventionsAll518-570
8Session ModelBounded units of agent work — lifecycle (create → execute → close → archive), tiers, SITREP, next-session prompt, 75% ruleOperations572-664
9Mission SystemMulti-session work decomposition — objectives, acceptance criteria, stages, handoff protocolOperations666-713
10Context Librarywhat/context/ — topic organization, context subtypes (research, guide, core), token budget awarenessOperations715-759
11Coordination Protocolwho/coordination/ — cross-agent notes, urgency levels (urgent/info/fyi), ephemeral by designMulti-agent761-789
12Template SystemGraduated template sets (starter/standard/full), template naming and conventionsExtension+791-827
13Collision PreventionThree tiers: universal (frontmatter attribution), sync (file safety tiers), multi-agent (coordination + scope declarations)Operations829-887
14Content-as-Code PipelinesFolder-based workflows — file location IS processing state, pipeline structure, stage AGENTS.mdExtension+889-939
15Archive & VersioningArchive patterns for sync vs. git environments, retention, CLAUDE.md version trackingReference941-970
16Tool Integration TiersThree tiers: core standard (Tier 1, universal), frontmatter querying (Tier 2), environment-specific (Tier 3)Reference972-1028
17Error & Recovery ProtocolThree-tier response: data integrity (STOP), state inconsistency (fix + log), process issues (workaround + backlog)Operations1030-1064
18Success CriteriaMinimum viable (cold start, handoff, integrity), recommended (fork, scale, consistency), aspirational (network, collision safety, dual-audience)Contributor1066-1116
19Optional ExtensionsMachine registry, backlog, skill files, testing/CI awareness, reference code, ADRsExtension+1118-1198
20AppendicesPersona framework (App A), aggregation points (App B), deferred topics (App C), decision traceability matrix (App D — 40 decisions)Contributor1200-1336

Persona key: All = everyone reads this. Extension+ = extension builders and contributors. Operations = anyone running sessions/missions. Multi-agent = concurrent agent environments. Reference = consult when needed. Contributor = standard contributors.


3. When to Read the Design Document

adna_design.md is the companion “why” document. It explains the rationale behind design decisions — why three legs, why these governance files, why these trade-offs. Read it when you want:

  • Rationale for why the standard works the way it does
  • Worked examples of deployment patterns (standalone, nested, federated)
  • Trade-off analysis behind structural decisions

The design document is not required for operational use. The standard tells you what to do; the design document tells you why.


4. Skill vs. Lattice: When to Use Which

aDNA has two constructs that both deal with “reusable capabilities” — skill files and skill-type lattices. They serve different purposes and live in different locations.

Comparison

DimensionSkill FileSkill-Type Lattice
Locationhow/skills/skill_<name>.mdwhat/lattices/<name>.lattice.yaml
FormatMarkdown with procedural stepsYAML directed graph with nodes and edges
PurposeAgent recipe — step-by-step instructionsComposable computational unit — executable DAG
When to createYou have a repeatable procedure an agent should followYou need a composable, publishable, executable workflow
ExecutionAgent reads and follows the stepsRuntime engine traverses the DAG
RegistryNot publishable (local to the vault)Publishable via latlab lattice publish
Promotion pathCan be promoted to a lattice via skill_lattice_publishAlready a lattice — can be composed with other lattices

Decision Rule

Start with a skill file. If the procedure needs to be published to a registry, composed with other lattices, or executed by a runtime engine, promote it to a lattice_type: skill lattice.

The promotion path is documented in how/skills/skill_lattice_publish.md. Most agent recipes stay as skill files — lattice promotion is for procedures that need computational composability.

Examples

ScenarioUseWhy
”Deploy this service in 5 steps”Skill fileAgent follows the steps — no DAG needed
”Run ESM-2 embedding → clustering → visualization”LatticeComputational pipeline — needs runtime execution
”Review and audit context quality”Skill fileProcedural checklist — agent walks through it
”Compose protein design with docking and scoring”LatticeMulti-module DAG — needs composability with other lattices

5. Quick Reference

“I want to…”

GoalWhere to look
Set up my first vault§3-5 of the standard, or the README Quick Start
Add a new entity type§6 (Naming) + §7 (Frontmatter) + §19 (Extensions)
Track sessions§8 (Session Model)
Run a multi-session project§9 (Mission System)
Write an agent skillhow/skills/AGENTS.md + §19.3, then this guide’s §4 for lattice promotion
Build a pipeline§14 (Content-as-Code Pipelines)
Understand collision prevention§13 (Collision Prevention)
Evaluate aDNA for my projectadna_design.md — the “why” document
Add aDNA to an existing codebasemigration_guide.md
Use aDNA without Obsidianagent_first_guide.md
Manage multiple aDNA projectsprojects_folder_pattern.md — workspace pattern with agent-guided scaffolding

Cross-References