@mnstry/atelier 0.2.0-alpha.14 → 0.2.0-alpha.16

package/docs/{install.md → start/install.md}

@@ -18,7 +18,7 @@ Git repository access is the hard read boundary for source files. Local
 from anyone who can read the repository.
 
 For adapters whose source repositories live elsewhere, see
-[project options](project-options.md) for shared CLI overrides, precedence and
+[project options](../reference/project-options.md) for shared CLI overrides, precedence and
 resolution diagnostics. Moving a repository does not change its read authority.
 
 Two command forms ship, and each has a place. Inside an installed
@@ -30,7 +30,7 @@ npm name `atelier` belongs to an unrelated third-party package, so a bare
 
 ## Install shape
 
-The registry is the distribution channel of record, as `docs/continuity.md`
+The registry is the distribution channel of record, as `docs/reference/continuity.md`
 commits:
 
 ```bash
@@ -256,7 +256,7 @@ and `setup.exclude`, which `adopt --include` and `adopt --exclude` record.
   Adoption wrote them and the `monorepo` profile requires `--include`, but
   until this release nothing read them. Giving them their meaning does not
   widen the contract. A new field, or a list, would widen a closed object,
-  which [contract stability](contract-stability.md) makes a new major version.
+  which [contract stability](../reference/contract-stability.md) makes a new major version.
 
 Each value is a path pattern relative to the folder that holds
 `atelier.project.json`, in the dialect the boundary policy's `forbiddenPaths`
@@ -287,13 +287,13 @@ are reviewable. Refresh it from inside the copied workspace after choosing a
 registry or Git tag install. Local tarballs remain release-audit and
 smoke-test tools; they are not the default install path.
 
-See `docs/tenant-readiness.md` for the readiness review format and
-`docs/upgrade.md` for the full upgrade flow and boundary review checklist.
+See `docs/guides/tenant-readiness.md` for the readiness review format and
+`docs/guides/upgrade.md` for the full upgrade flow and boundary review checklist.
 
 ## External source adapters and local review
 
 Use `atelier init --template external-project --target NEW_DIRECTORY` for the
-invented adapter/source starter. See [local review](local-review.md) for the
+invented adapter/source starter. See [local review](../guides/local-review.md) for the
 complete installed workflow, source ownership, asserted identity and save/resume.
 `atelier lock provenance` distinguishes declared install origin, observed package
 bytes and verified clean-checkout binding. It never substitutes the consumer

package/docs/{knowledge-setup.md → start/knowledge-setup.md}

@@ -49,7 +49,7 @@ boundary. These commands do not implement recipient authorization or sharing.
    records cannot satisfy retrieval coverage. Duplicate mappings of a predicate
    and concept pair are refused; use assertion records for distinct meanings.
 5. Keep a small permitted slice of originals. Use Markdown front matter or
-   adjacent sidecars as described in [the source graph](knowledge-graph.md).
+   adjacent sidecars as described in [the source graph](../reference/knowledge-graph.md).
    Use `atelier adopt` for an existing workspace; do not initialize over it.
    Copy and adapt the starter plan, then use `--plan FILE` if it lives elsewhere.
 6. Compare retrieval on the questions before adding a model, vector index, or
@@ -64,7 +64,7 @@ boundary. These commands do not implement recipient authorization or sharing.
 For a real workspace, replace every fictional record, role, and case. In the
 starter, roles are examples and source rights are assumed only for its invented
 content. Add repository boundary policies and hooks through the existing
-[boundary workflow](repo-boundary-guard.md) when collaborating across trust domains.
+[boundary workflow](../reference/repo-boundary-guard.md) when collaborating across trust domains.
 Use actual access controls at the consuming host.
 
 ## Domain ontology and source graph are different layers
@@ -140,7 +140,7 @@ not a claim that the real-world fact does not exist. When search misses a
 qualification that a source owner has selected, a trusted host can read the
 complete cited unit exactly from an ingestion plan that includes the source
 with a completed attempt; see
-[read a complete selected citation](evidence-navigation.md#read-a-complete-selected-citation).
+[read a complete selected citation](../reference/evidence-navigation.md#read-a-complete-selected-citation).
 The line locations in this packet are not ingestion `line` locators: ingestion
 also splits on a lone CR and removes a leading BOM (U+FEFF). Map them
 explicitly; a wrong mapping fails safe, because the hash check withholds the
@@ -197,14 +197,14 @@ for that evidence.
 Use `atelier dev --knowledge` after graph/build to work through Onboard, Model,
 Deepen, Apply, and Learn. The browser and `knowledge session` CLI share
 source-bound private drafts, confirmation, and recovery. See
-[knowledge workspaces](knowledge-workspace.md) for the complete flow and limits.
+[knowledge workspaces](../guides/knowledge-workspace.md) for the complete flow and limits.
 
 ## Recording a host's semantic extraction
 
 `atelier knowledge semantic` records an extraction that your own tool or model
 ran, so a receiver can review it against the exact source. Atelier never runs
 the extraction. The runner, its request shapes and the receiver journey are
-described in [semantic operation](semantic-operation.md); this section covers
+described in [semantic operation](../reference/semantic-operation.md); this section covers
 the command.
 
 - Run it in the Git workspace where `atelier ingest` planned and ran the

package/docs/{research-starter-quickstart.md → start/research-starter-quickstart.md}

@@ -1,7 +1,7 @@
 # Start a research workspace
 
 This packet works with any topic and research tool. Read
-[the six-stage research starter](research-starter.md) for the prompts. The package
+[the six-stage research starter](../guides/research-starter.md) for the prompts. The package
 provides local evidence custody, governance, skills and contracts; your selected
 research tool and reviewers supply research and judgment.
 
@@ -45,11 +45,11 @@ compatibility and plan a destination-specific adoption. An installed skill is
 not automatically active in an agent. Keep local instructions and custom skills;
 review a concrete adoption plan before applying its exact digest.
 
-Use [ingestion](ingestion.md) for bounded local captures and
-[Knowledge and Build](learning-harnesses.md) for the current governed
-workflow. Practical lessons use [Practical Judgment](practical-judgment.md).
-[Trackables](trackables.md), [Interaction and Reflection](interaction-and-reflection.md)
-and [Coordination](coordination.md) describe supported reference profiles and
+Use [ingestion](../guides/ingestion.md) for bounded local captures and
+[Knowledge and Build](../guides/learning-harnesses.md) for the current governed
+workflow. Practical lessons use [Phronesis — practical judgment](../reference/phronesis.md).
+[Trackables](../reference/trackables.md), [Interaction and Reflection](../reference/interaction-and-reflection.md)
+and [Coordination](../reference/coordination.md) describe supported reference profiles and
 what an actual host must implement.
 
 ## What successful completion looks like

package/fixtures/atelier-architecture/catalog/invalid/document.json

@@ -27,9 +27,9 @@
     {
       "id": "practical-judgment",
       "kind": "responsibility",
-      "label": "Practical Judgment",
+      "label": "Phronesis",
       "aliases": [
-        "Phronesis"
+        "Practical Judgment"
       ],
       "purpose": "Discern fitting action, cultivate practice and learn from consequences.",
       "implementation": [

package/fixtures/atelier-architecture/catalog/valid/document.json

@@ -27,9 +27,9 @@
     {
       "id": "practical-judgment",
       "kind": "responsibility",
-      "label": "Practical Judgment",
+      "label": "Phronesis",
       "aliases": [
-        "Phronesis"
+        "Practical Judgment"
       ],
       "purpose": "Discern fitting action, cultivate practice and learn from consequences.",
       "implementation": [

package/fixtures/graph-view/synthetic-authorized-input.v1.json

@@ -0,0 +1,437 @@
+{
+  "producerVersion": "0.2.0-alpha.15+synthetic-graph-view",
+  "completeness": "complete",
+  "sourceSnapshot": {
+    "repositories": [
+      {
+        "repoId": "synthetic:garden",
+        "head": "1111111111111111111111111111111111111111",
+        "tree": "3333333333333333333333333333333333333333",
+        "dirty": false,
+        "scope": {
+          "base": "",
+          "include": null,
+          "exclude": null
+        },
+        "files": [
+          {
+            "path": "content/counterexample.md",
+            "rawDigest": "sha256:e7662a31a5f67ed5043b3e82bddab867e8e6e0d91bfbc1ad7fe29ea4af1d29e3",
+            "byteLength": 64
+          },
+          {
+            "path": "content/observation.md",
+            "rawDigest": "sha256:06ed304c28bd2698268cfa48628caa5db7db83256909c4f6d0cd73fd8579e423",
+            "byteLength": 70
+          },
+          {
+            "path": "content/trial.md",
+            "rawDigest": "sha256:d28e14da89ff1d5bc422c3402e8ceb0ce3853f39452a2e424769c7f5a5c77a7f",
+            "byteLength": 54
+          }
+        ],
+        "digest": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "inputs": {
+          "config": null,
+          "plan": null
+        }
+      },
+      {
+        "repoId": "synthetic:workshop",
+        "head": "2222222222222222222222222222222222222222",
+        "tree": "4444444444444444444444444444444444444444",
+        "dirty": false,
+        "scope": {
+          "base": "",
+          "include": null,
+          "exclude": null
+        },
+        "files": [
+          {
+            "path": "content/observation.md",
+            "rawDigest": "sha256:384baef02239aa85715b0946ea2beb1664428771fb261d50e0d1cb7fc7ac440a",
+            "byteLength": 68
+          }
+        ],
+        "digest": "sha256:4440838eba940cd70177eba5078a368596e67af183d7745f9f012b2ef2b623fe",
+        "inputs": {
+          "config": null,
+          "plan": null
+        }
+      }
+    ]
+  },
+  "accessContext": {
+    "proofRef": "synthetic-only-not-an-access-grant",
+    "authorizedRepoIds": [
+      "synthetic:garden",
+      "synthetic:workshop"
+    ],
+    "grantRevision": "synthetic-grant-r1",
+    "policyRevision": "synthetic-policy-r1",
+    "expiresAt": "2031-01-01T00:00:00Z",
+    "filter": "synthetic-fixture"
+  },
+  "nodes": [
+    {
+      "ref": {
+        "repoId": "synthetic:garden",
+        "localId": "trial"
+      },
+      "sourceKind": "document",
+      "title": "Trial outline",
+      "summary": "One small trial needs two observations.",
+      "classification": "classified",
+      "lifecycle": "active",
+      "tags": [
+        "synthetic",
+        "concept:trial"
+      ],
+      "sourceRef": {
+        "repoId": "synthetic:garden",
+        "path": "content/trial.md",
+        "revision": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "digest": "sha256:d28e14da89ff1d5bc422c3402e8ceb0ce3853f39452a2e424769c7f5a5c77a7f"
+      },
+      "displayEligible": true
+    },
+    {
+      "ref": {
+        "repoId": "synthetic:garden",
+        "localId": "observation"
+      },
+      "sourceKind": "evidence",
+      "title": "First observation",
+      "summary": "A single observation supports continuing carefully.",
+      "classification": "classified",
+      "lifecycle": "active",
+      "tags": [
+        "synthetic",
+        "concept:trial"
+      ],
+      "sourceRef": {
+        "repoId": "synthetic:garden",
+        "path": "content/observation.md",
+        "revision": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "digest": "sha256:06ed304c28bd2698268cfa48628caa5db7db83256909c4f6d0cd73fd8579e423"
+      },
+      "displayEligible": true
+    },
+    {
+      "ref": {
+        "repoId": "synthetic:garden",
+        "localId": "counterexample"
+      },
+      "sourceKind": "evidence",
+      "title": "Counterexample",
+      "summary": "The alternate setting did not repeat the result.",
+      "classification": "classified",
+      "lifecycle": "active",
+      "tags": [
+        "synthetic",
+        "concept:trial"
+      ],
+      "sourceRef": {
+        "repoId": "synthetic:garden",
+        "path": "content/counterexample.md",
+        "revision": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "digest": "sha256:e7662a31a5f67ed5043b3e82bddab867e8e6e0d91bfbc1ad7fe29ea4af1d29e3"
+      },
+      "displayEligible": true
+    },
+    {
+      "ref": {
+        "repoId": "synthetic:workshop",
+        "localId": "observation"
+      },
+      "sourceKind": "evidence",
+      "title": "Second observation",
+      "summary": "A separate source has the same local identifier.",
+      "classification": "classified",
+      "lifecycle": "active",
+      "tags": [
+        "synthetic",
+        "concept:trial"
+      ],
+      "sourceRef": {
+        "repoId": "synthetic:workshop",
+        "path": "content/observation.md",
+        "revision": "sha256:4440838eba940cd70177eba5078a368596e67af183d7745f9f012b2ef2b623fe",
+        "digest": "sha256:384baef02239aa85715b0946ea2beb1664428771fb261d50e0d1cb7fc7ac440a"
+      },
+      "displayEligible": true
+    }
+  ],
+  "edges": [
+    {
+      "edgeId": "synthetic-edge-0",
+      "source": {
+        "repoId": "synthetic:garden",
+        "localId": "trial"
+      },
+      "target": {
+        "repoId": "synthetic:garden",
+        "localId": "observation"
+      },
+      "predicate": "supports",
+      "family": "source-declaration",
+      "acceptanceState": "active",
+      "assurance": "source-declaration",
+      "supportRefs": [
+        "synthetic-evidence-0"
+      ],
+      "reviewRefs": [],
+      "sourceRef": "synthetic-evidence-0",
+      "recordDigest": "sha256:bfb01fc86aa35a784161a485c28afa3dec85a716e731ee144926be44a22eaf77",
+      "policyDigest": "sha256:020d7bf97d02339fdbea3b0dd783d600dbe12ff3bcf27a4ddca7728299944ae4",
+      "verification": {
+        "checkedAt": "2030-01-01T00:00:00Z"
+      },
+      "qualifications": []
+    },
+    {
+      "edgeId": "synthetic-edge-1",
+      "source": {
+        "repoId": "synthetic:garden",
+        "localId": "trial"
+      },
+      "target": {
+        "repoId": "synthetic:garden",
+        "localId": "observation"
+      },
+      "predicate": "supports",
+      "family": "source-declaration",
+      "acceptanceState": "active",
+      "assurance": "source-declaration",
+      "supportRefs": [
+        "synthetic-evidence-repeat"
+      ],
+      "reviewRefs": [],
+      "sourceRef": "synthetic-evidence-repeat",
+      "recordDigest": "sha256:df594d71a145abdc3d2b8d6c6fa910dd4bb21f63de731ecd11fe97b6ff6ce691",
+      "policyDigest": "sha256:020d7bf97d02339fdbea3b0dd783d600dbe12ff3bcf27a4ddca7728299944ae4",
+      "verification": {
+        "checkedAt": "2030-01-01T00:00:00Z"
+      },
+      "qualifications": []
+    },
+    {
+      "edgeId": "synthetic-edge-2",
+      "source": {
+        "repoId": "synthetic:garden",
+        "localId": "counterexample"
+      },
+      "target": {
+        "repoId": "synthetic:garden",
+        "localId": "trial"
+      },
+      "predicate": "contradicts",
+      "family": "source-declaration",
+      "acceptanceState": "active",
+      "assurance": "source-declaration",
+      "supportRefs": [
+        "synthetic-evidence-2"
+      ],
+      "reviewRefs": [],
+      "sourceRef": "synthetic-evidence-2",
+      "recordDigest": "sha256:a5daf75309e66ad7df3c4d53c016403fc60f72e0d9f92900ba008306a818de64",
+      "policyDigest": "sha256:020d7bf97d02339fdbea3b0dd783d600dbe12ff3bcf27a4ddca7728299944ae4",
+      "verification": {
+        "checkedAt": "2030-01-01T00:00:00Z"
+      },
+      "qualifications": []
+    },
+    {
+      "edgeId": "synthetic-edge-3",
+      "source": {
+        "repoId": "synthetic:garden",
+        "localId": "observation"
+      },
+      "target": {
+        "repoId": "synthetic:garden",
+        "localId": "counterexample"
+      },
+      "predicate": "links_to",
+      "family": "hyperlink",
+      "acceptanceState": "active",
+      "assurance": "navigation",
+      "supportRefs": [
+        "synthetic-evidence-1"
+      ],
+      "reviewRefs": [],
+      "sourceRef": "synthetic-evidence-1",
+      "recordDigest": "sha256:ec85738f376e8fcc961365327c5a7524d802aadc4ac349cb0c1f6055a73d0943",
+      "policyDigest": "sha256:020d7bf97d02339fdbea3b0dd783d600dbe12ff3bcf27a4ddca7728299944ae4",
+      "verification": {
+        "checkedAt": "2030-01-01T00:00:00Z"
+      },
+      "qualifications": []
+    }
+  ],
+  "evidence": [
+    {
+      "evidenceId": "synthetic-evidence-0",
+      "sourceRef": {
+        "repoId": "synthetic:garden",
+        "path": "content/trial.md",
+        "revision": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "digest": "sha256:d28e14da89ff1d5bc422c3402e8ceb0ce3853f39452a2e424769c7f5a5c77a7f",
+        "locator": {
+          "range": {
+            "start": 0,
+            "end": 4,
+            "byteStart": 0,
+            "byteEnd": 4
+          }
+        }
+      },
+      "verification": "verified-source"
+    },
+    {
+      "evidenceId": "synthetic-evidence-1",
+      "sourceRef": {
+        "repoId": "synthetic:garden",
+        "path": "content/observation.md",
+        "revision": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "digest": "sha256:06ed304c28bd2698268cfa48628caa5db7db83256909c4f6d0cd73fd8579e423",
+        "locator": {
+          "range": {
+            "start": 0,
+            "end": 4,
+            "byteStart": 0,
+            "byteEnd": 4
+          }
+        }
+      },
+      "verification": "verified-source"
+    },
+    {
+      "evidenceId": "synthetic-evidence-2",
+      "sourceRef": {
+        "repoId": "synthetic:garden",
+        "path": "content/counterexample.md",
+        "revision": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "digest": "sha256:e7662a31a5f67ed5043b3e82bddab867e8e6e0d91bfbc1ad7fe29ea4af1d29e3",
+        "locator": {
+          "range": {
+            "start": 0,
+            "end": 4,
+            "byteStart": 0,
+            "byteEnd": 4
+          }
+        }
+      },
+      "verification": "verified-source"
+    },
+    {
+      "evidenceId": "synthetic-evidence-3",
+      "sourceRef": {
+        "repoId": "synthetic:workshop",
+        "path": "content/observation.md",
+        "revision": "sha256:4440838eba940cd70177eba5078a368596e67af183d7745f9f012b2ef2b623fe",
+        "digest": "sha256:384baef02239aa85715b0946ea2beb1664428771fb261d50e0d1cb7fc7ac440a",
+        "locator": {
+          "range": {
+            "start": 0,
+            "end": 4,
+            "byteStart": 0,
+            "byteEnd": 4
+          }
+        }
+      },
+      "verification": "verified-source"
+    },
+    {
+      "evidenceId": "synthetic-evidence-repeat",
+      "sourceRef": {
+        "repoId": "synthetic:garden",
+        "path": "content/trial.md",
+        "revision": "sha256:f3c72ec37d8d8fe01ef00e218c2dfcd46ffbf9cdb35dd568b335c3561ea04c98",
+        "digest": "sha256:d28e14da89ff1d5bc422c3402e8ceb0ce3853f39452a2e424769c7f5a5c77a7f",
+        "locator": {
+          "pointer": "/kg/relations/supports/1"
+        }
+      },
+      "verification": "verified-source"
+    }
+  ],
+  "questions": [
+    {
+      "questionId": "synthetic-question-1",
+      "title": "Which trial needs more evidence?",
+      "decision": "Choose the next observation before continuing the trial.",
+      "nodeRefs": [
+        {
+          "repoId": "synthetic:garden",
+          "localId": "trial"
+        },
+        {
+          "repoId": "synthetic:garden",
+          "localId": "observation"
+        },
+        {
+          "repoId": "synthetic:garden",
+          "localId": "counterexample"
+        }
+      ],
+      "evidenceRefs": [
+        "synthetic-evidence-0",
+        "synthetic-evidence-1"
+      ],
+      "contradictingRefs": [
+        "synthetic-evidence-2"
+      ],
+      "coverage": "partial",
+      "omissionState": "none",
+      "gaps": [
+        "The sources do not establish repeatability."
+      ]
+    },
+    {
+      "questionId": "synthetic-question-unknown",
+      "title": "Will the trial work next year?",
+      "decision": "Abstain until later observations exist.",
+      "nodeRefs": [],
+      "evidenceRefs": [],
+      "contradictingRefs": [],
+      "coverage": "abstain",
+      "omissionState": "none",
+      "gaps": [
+        "No later observation is available."
+      ]
+    }
+  ],
+  "diagnostics": [
+    {
+      "diagnosticId": "synthetic-diagnostic-1",
+      "code": "more-evidence-needed",
+      "severity": "info",
+      "action": "Record a second observation.",
+      "nodeRefs": [
+        {
+          "repoId": "synthetic:garden",
+          "localId": "trial"
+        }
+      ],
+      "evidenceRefs": [
+        "synthetic-evidence-0"
+      ]
+    }
+  ],
+  "capabilities": {
+    "maxSlice": 500,
+    "maxDepth": 2,
+    "sourceReads": false,
+    "proposalIntents": [
+      "proposeModelChange"
+    ],
+    "queries": [
+      "metadata-search",
+      "neighborhood",
+      "question",
+      "source-impact"
+    ],
+    "read": true,
+    "export": true
+  }
+}

package/fixtures/graph-view/synthetic-view.v1.json

@@ -0,0 +1 @@
+{"accessContext":{"authorizedRepoIds":["synthetic:garden","synthetic:workshop"],"expiresAt":"2031-01-01T00:00:00Z","filter":"synthetic-fixture","grantRevision":"synthetic-grant-r1","policyRevision":"synthetic-policy-r1","proofRef":"synthetic-only-not-an-access-grant"},"capabilities":{"export":true,"maxDepth":2,"maxSlice":500,"proposalIntents":["proposeModelChange"],"queries":["metadata-search","neighborhood","question","source-impact"],"read":true,"sourceReads":false},"completeness":"complete","diagnostics":[{"action":"Record a second 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package/fixtures/knowledge-health/workshop/README.md

@@ -15,6 +15,6 @@ This is an example proposal for the participant to inspect, not an assistant res
 
 Create a disposable copy using the installed host's supported example-copy operation. If the host has not supplied that operation, copy this folder through your ordinary file manager into a new directory, then initialize that directory as a Git repository with `git init`. Keep `.atelier-local/` and `output/` ignored before opening a native draft store. Never open the package's installed files as a writable workspace.
 
-Read the [exercise](../../../docs/knowledge-health/exercise.md) before changing anything. Once the source owner applies a chosen revision, reread the exact source and refresh the plan's corresponding expected-evidence hash through the installed owning tool. Run the same question evaluation and relationship check again. Do not report a verified evidence match from an old hash or silently replace the participant's historical finding reference.
+Read the [exercise](../../../docs/knowledge-health/quickstart.md) before changing anything. Once the source owner applies a chosen revision, reread the exact source and refresh the plan's corresponding expected-evidence hash through the installed owning tool. Run the same question evaluation and relationship check again. Do not report a verified evidence match from an old hash or silently replace the participant's historical finding reference.
 
 The two commands `git init` and `node --version` are ordinary prerequisite checks. The actual assessment, guided-host, source-application and reassessment entry commands are release-owner joins; none is guessed here.

package/fixtures/templates/local-library.v1.json

@@ -68,7 +68,9 @@
       "0.2.0-alpha.10",
       "0.2.0-alpha.12",
       "0.2.0-alpha.13",
-      "0.2.0-alpha.14"
+      "0.2.0-alpha.14",
+      "0.2.0-alpha.15",
+      "0.2.0-alpha.16"
     ],
     "packRefs": []
   },