Align internal documentation and maintained examples

README.md

@@ -25,8 +25,8 @@ This requires resolvable `pipeline.yml`, `campaign.yml`, and concrete
   safe remedies.
 - [Integration contracts](docs/integrations/) — external tools, formats, and
   compatibility expectations.
-- [Maintained examples](examples/) — complete copyable configuration and input
-  files.
+- [Maintained examples](examples/README.md) — complete copyable configuration
+  and input files.
 
 ## Maintainer Documentation
 

docs/config.md

@@ -274,10 +274,6 @@ Audio rules:
 
 ## Maintained Examples
 
-- `examples/pipeline.minimal.yml`
-- `examples/pipeline.production.yml`
-- `examples/pipeline.full.annotated.yml`
-- `examples/campaigns/sample-campaign/campaign.yml`
-- `examples/session.local-audio.yml`
-- `examples/session.s3-audio.yml`
-- `examples/session.template.yml`
+See the [maintained examples index](../examples/README.md) for complete pipeline,
+campaign, session, template, and input fixtures. Keep complete copyable files
+there rather than duplicating them in this reference.

docs/development.md

@@ -24,7 +24,7 @@ polished transcripts and generated artifacts. Start with the
 | Pipeline sequencing or the behavior of a stage | [Internal Overview](internal/overview.md) and its focused stage documents | The overview owns the implemented stage inventory and routes to each stage contract. |
 | Adapters or external tool contracts | [Adapter Internals](internal/adapters.md) and [Integration Contracts](integrations/README.md) | The internal guide owns adapter composition and mechanics; integration documents own external formats and protocols. |
 | Manifests, artifacts, workspace paths, or publish behavior | [Manifest Internals](internal/manifest.md), [Artifact Internals](internal/artifacts.md), [Workspace Internals](internal/workspace.md), [Publish Internals](internal/stage-publish.md), and [Operations](operations.md) | These separate implementation state and resolution from operator-visible layout and lifecycle. |
-| Maintained configuration or input examples | [Configuration](config.md) and [Examples](../examples/) | The reference owns field meanings; the examples directory owns complete copyable files. |
+| Maintained configuration or input examples | [Configuration](config.md) and [Examples](../examples/README.md) | The reference owns field meanings; the examples directory owns complete copyable files. |
 | Proposed or unimplemented behavior | [Roadmap](roadmap/) | Future work belongs only in roadmap documentation until implemented. |
 
 For an existing subsystem, also inspect its focused tests and package-level

docs/integrations/audita.md

@@ -54,5 +54,6 @@ Operator-selected values are defined under `pipeline.audita.*` in the
 [configuration reference](../config.md#pipeline).
 
 Maintained example with Audita config:
-- `examples/pipeline.full.annotated.yml`
-- `examples/pipeline.production.yml`
+
+- [Full annotated pipeline](../../examples/pipeline.full.annotated.yml)
+- [Production-shaped pipeline](../../examples/pipeline.production.yml)

docs/integrations/scriptorium.md

@@ -63,5 +63,6 @@ per-artifact settings under `pipeline.scriptorium.artifacts.*`, in the
 [configuration reference](../config.md#pipeline).
 
 Maintained examples with Scriptorium config:
-- `examples/pipeline.full.annotated.yml`
-- `examples/pipeline.production.yml`
+
+- [Full annotated pipeline](../../examples/pipeline.full.annotated.yml)
+- [Production-shaped pipeline](../../examples/pipeline.production.yml)

docs/integrations/seriatim.md

@@ -55,5 +55,6 @@ Operator-selected values are defined under `pipeline.seriatim.*` and
 [configuration reference](../config.md#pipeline).
 
 Maintained examples with Seriatim config:
-- `examples/pipeline.full.annotated.yml`
-- `examples/pipeline.production.yml`
+
+- [Full annotated pipeline](../../examples/pipeline.full.annotated.yml)
+- [Production-shaped pipeline](../../examples/pipeline.production.yml)

docs/internal/adapters.md

@@ -1,12 +1,17 @@
 # Internal: Adapters
 
 ## Purpose
-Define external integration boundaries and default adapter wiring used by app/stage orchestration.
+
+Explain the adapter interfaces and production composition used by application
+and stage orchestration. Externally observable protocols and formats belong in
+the [integration contracts](../integrations/).
 
 ## Adapter Boundaries
+
 Narratio stage logic depends on adapter interfaces, not transport-specific details.
 
 Primary adapters:
+
 - `whisperx.Client`
 - `seriatim.Runner`
 - `audita.Runner`
@@ -15,17 +20,22 @@ Primary adapters:
 - `notify.Sender`
 
 ## Ownership
+
 Adapters own:
+
 - HTTP/subprocess/SDK argument and transport details.
 - Backend-specific request/response mapping.
 
 Adapters do not own:
+
 - stage ordering/skip/force logic;
 - manifest transitions;
 - canonical path policy.
 
 ## Default Wiring
+
 `internal/app/runner.go` initializes default adapters when not injected:
+
 - WhisperX HTTP client from pipeline config.
 - Seriatim subprocess runner.
 - Audita subprocess runner.
@@ -33,17 +43,29 @@ Adapters do not own:
 - Noop notifier (`notify.NoopSender`).
 - Object store only when required by selected stages/config.
 
-Object-store construction goes through `newCommandObjectStore`, which loads configured filesystem secrets before adapter initialization.
+Object-store construction goes through `newCommandObjectStore`, which loads
+configured filesystem secrets before adapter initialization.
 
 ## Failure Semantics
+
 - Constructor errors fail stage execution setup early.
 - Runtime adapter errors propagate to stage code and then manifest failure handling.
 - Subprocess adapters persist stage logs/generated configs through stage-managed paths.
 
-## Test Surfaces
+## Implementation And Tests
+
+- Composition: `internal/app/runner.go`, `internal/app/object_store.go`
+- Shared subprocess mechanics: `internal/adapters/subprocess`
+- Focused adapters: `internal/adapters/{whisperx,seriatim,audita,scriptorium,storage,notify}`
 - `internal/adapters/whisperx/http_test.go`
 - `internal/adapters/seriatim/subprocess_test.go`
 - `internal/adapters/audita/subprocess_test.go`
 - `internal/adapters/scriptorium/subprocess_test.go`
 - `internal/adapters/storage/*_test.go`
 - `internal/app/runner_test.go`
+
+See the [WhisperX](../integrations/whisperx.md),
+[Seriatim](../integrations/seriatim.md), [Audita](../integrations/audita.md),
+and [Scriptorium](../integrations/scriptorium.md) contracts before changing an
+externally visible boundary. Operator-selected values belong in
+[Configuration](../config.md).

docs/internal/artifacts.md

@@ -1,17 +1,28 @@
 # Internal: Artifacts
 
 ## Purpose
-Define canonical artifact IDs, runtime catalog behavior, source resolution rules, and shared current-state mechanics used by app and previous-cache code.
+
+Explain the artifact registry, runtime catalog, resolver, previous-input
+requirements, and shared remote current-state mechanics implemented by
+`internal/artifacts`. Configuration fields that accept source IDs belong in
+[Configuration](../config.md); physical placement belongs in
+[Operations](../operations.md).
 
 ## Built-in Source IDs
 
-- `narratio.transcript.base` -> `transcripts/base.json` (`merge`)
-- `narratio.transcript.polished` -> `transcripts/polished.json` (`polish`)
-- `narratio.transcript.final` -> `transcripts/final.json` (`normalize`)
-- `narratio.transcript.final_trimmed` -> `transcripts/final.trimmed.json` (`trim`)
-- `narratio.transcript.final_markdown` -> `transcripts/final.md` (`render`)
-- `narratio.transcript.final_trimmed_markdown` -> `transcripts/final.trimmed.md` (`render`)
-- `narratio.bounds.session` -> `artifacts/session_bounds.json` (`trim`)
+The internal registry recognizes these stable built-in source IDs:
+
+- `narratio.transcript.base`
+- `narratio.transcript.polished`
+- `narratio.transcript.final`
+- `narratio.transcript.final_trimmed`
+- `narratio.transcript.final_markdown`
+- `narratio.transcript.final_trimmed_markdown`
+- `narratio.bounds.session`
+
+Registry entries bind each ID to its producer, output kind, canonical fallback,
+and content validator. The focused stage documents own their input/output flow;
+[Configuration](../config.md) owns where operators may select these IDs.
 
 ## Configured and Previous-Session Sources
 
@@ -72,7 +83,8 @@ Validation by content type:
 
 ## Current-State Helpers
 
-Artifacts package owns shared remote current-state loading mechanics used by restore, status/validate checks, and previous-cache planning.
+Artifacts package owns shared remote current-state loading mechanics used by
+restore, status and validation checks, and previous-cache planning.
 
 Core helpers:
 
@@ -107,9 +119,27 @@ Caller policy is intentionally outside artifacts helpers:
 - spool/cache paths;
 - S3 session/run/current-state key layout.
 
+See [Workspace Internals](workspace.md) for how callers consume local helpers
+and [Operations](../operations.md#local-state-layout) for the authoritative
+physical layout.
+
 ## Invariants
 
 - source ID formats are stable contracts;
 - artifact resolution is deterministic and manifest-aware;
 - previous-session source resolution in `analyze` is local-only;
 - remote current-state key construction remains centralized in artifacts helpers.
+
+## Implementation And Tests
+
+- Registry and resolution: `internal/artifacts/artifact_resolver.go`,
+  `internal/artifacts/catalog.go`, `internal/artifacts/transcripts.go`
+- Current state: `internal/artifacts/current_state.go`
+- Paths and keys: `internal/artifacts/paths.go`,
+  `internal/artifacts/s3_keys.go`
+- Previous requirements: `internal/artifacts/previous_requirements.go`
+- Tests: `internal/artifacts/artifact_resolver_test.go`,
+  `internal/artifacts/catalog_test.go`,
+  `internal/artifacts/current_state_test.go`,
+  `internal/artifacts/paths_model_test.go`,
+  `internal/artifacts/previous_requirements_test.go`

docs/internal/command-restore.md

@@ -1,21 +1,20 @@
 # Internal: Command Restore
 
 ## Purpose
-Define the implemented `narratio session restore` command contract:
 
-- committed remote current-state discovery;
-- deterministic restore planning;
-- safe local install semantics;
-- durable restore reporting.
+Explain the implemented restore discovery, planning, installation, and
+reporting flow in `internal/app`. User invocation belongs in
+[CLI](../cli.md#session-restore), and the operator recovery procedure and
+physical restore scope belong in
+[Operations](../operations.md#restore-workflow).
+
+Restore is split into explicit phases so remote authority, local conflict
+policy, and filesystem mutation can be tested independently.
 
 ## Discovery Contract
 
-Restore resolves remote committed state from the session publish current pointers:
-
-- `current/run_id.txt` (required, non-empty);
-- `current/manifest.json` (required, decodable).
-
-Current-state discovery uses shared artifacts-level mechanics and validates identity against the resolved request config:
+Discovery delegates current-state pointer and manifest loading to
+`internal/artifacts`, then validates the result against the resolved request:
 
 - campaign must match;
 - session ID must match.
@@ -34,26 +33,11 @@ Planner behavior:
 
 - remote list scope is the resolved session prefix;
 - remote-to-local mapping is traversal-safe;
-- actions are sorted deterministically by local relative path.
+- actions are sorted by local relative path and then remote key;
+- force converts differing local targets from conflicts to downloads.
 
-Restore scope from current remote state:
-
-- include `manifest.json`;
-- include `transcripts/**`;
-- include `artifacts/**`;
-- include `audio/**` only with `--include-audio`.
-
-Explicit exclusions from current remote state mapping:
-
-- `current/**`;
-- `runs/**`;
-- `logs/**`;
-- `reports/**`;
-- `config/**`;
-- `inputs/**`;
-- `previous/**`.
-
-Previous-cache files are planned separately through `previouscache.BuildPlan` when configured previous-session requirements exist.
+Previous-cache files are planned separately through `previouscache.BuildPlan`
+when configured previous-session requirements exist.
 
 ## Execution Contract
 
@@ -73,8 +57,9 @@ Audio restore path:
 
 ## Reporting Contract
 
-- `--dry-run`: prints summary only; no local writes.
-- non-dry-run: writes `reports/restore-latest.json`.
+- dry-run mode prints a summary and performs no local writes;
+- execution mode persists the canonical restore report described in
+  [Operations](../operations.md#restore-workflow);
 - report includes plan counts, per-action status, and execution failures.
 
 ## Invariants
@@ -82,3 +67,15 @@ Audio restore path:
 - restore uses committed remote current state as authority;
 - `current/run_id.txt` is the remote publish commit marker;
 - restore does not execute pipeline stages.
+
+## Implementation And Tests
+
+- Discovery: `internal/app/restore_discovery.go`
+- Planning: `internal/app/restore_plan.go`, `internal/previouscache`
+- Execution: `internal/app/restore_execute.go`
+- Reporting and command coordination: `internal/app/restore_report.go`,
+  `internal/app/restore.go`
+- Tests: `internal/app/restore_discovery_test.go`,
+  `internal/app/restore_plan_test.go`,
+  `internal/app/restore_execution_test.go`,
+  `internal/app/restore_workflow_test.go`

docs/internal/manifest.md

@@ -1,13 +1,15 @@
 # Internal: Manifest
 
 ## Purpose
-Define durable session state (`manifest.json`) and invocation state (`runs/{run_id}/manifest.json`) contracts.
+
+Explain the session-progress and invocation-audit models implemented by
+`internal/manifest`. Physical manifest placement belongs in
+[Operations](../operations.md#local-state-layout).
 
 ## Session Manifest
-Path:
-- `{workspace.root}/work/{campaign}/{session_id}/manifest.json`
 
-Primary model (`manifest.Manifest`):
+`manifest.Manifest` records:
+
 - identity (`session_id`, `campaign`, `run_id`)
 - local path metadata (`local_workdir`, `local_spool_dir`)
 - remote identity metadata (`s3_bucket`, `s3_session_prefix`, `s3_run_prefix`)
@@ -15,7 +17,8 @@ Primary model (`manifest.Manifest`):
 - durable `artifacts` records
 - per-stage `stages` map
 
-Stage status enum:
+The model admits these stage states:
+
 - `pending`
 - `running`
 - `succeeded`
@@ -25,10 +28,9 @@ Stage status enum:
 - `interrupted`
 
 ## Run Manifest
-Path:
-- `{workspace.root}/work/{campaign}/{session_id}/runs/{run_id}/manifest.json`
 
-Run model (`manifest.RunManifest`):
+`manifest.RunManifest` is created for each invocation and records:
+
 - invocation identity and `force` flag
 - requested stages
 - per-stage action (`run` or `skip`)
@@ -36,22 +38,40 @@ Run model (`manifest.RunManifest`):
 - overall run status (`running`, `succeeded`, `failed`)
 
 ## Persistence Semantics
+
 `manifest.LocalStore`:
+
 - validates loaded documents;
 - normalizes missing maps/stage records;
 - writes atomically via temp file + rename;
 - updates `updated_at` on save.
 
 ## Execution Semantics
-Runner updates both manifests per stage transition:
-- mark running
-- mark succeeded/failed/skipped
-- persist logs/generated config refs and metadata
+
+The application runner marks an executing stage running and then succeeded or
+failed in both manifests, persisting each transition. On success it records
+outputs, logs, generated configuration references, and metadata. A successful
+forced rerun marks only succeeded downstream session-stage records stale.
+
+When an already-succeeded stage is skipped, the invocation run manifest records
+the `skip` action and reason. The session manifest deliberately retains its
+existing succeeded record because it remains the cross-invocation progress
+authority.
 
 Session manifest is the authoritative stage-progress ledger across invocations.
 Run manifest is invocation-scoped audit state.
 
 ## Invariants
+
 - stage resume/skip decisions are session-manifest driven.
 - force reruns stale downstream succeeded stages.
 - run manifest does not replace session manifest as progress authority.
+
+## Implementation And Tests
+
+- Models and transitions: `internal/manifest/manifest.go`,
+  `internal/manifest/run_manifest.go`
+- Persistence and validation: `internal/manifest/store.go`
+- Package tests: `internal/manifest/*_test.go`
+- Assembled execution behavior: `internal/app/runner_test.go`,
+  `internal/app/run_stage_test.go`

docs/internal/overview.md

@@ -59,7 +59,8 @@ The implemented canonical order is:
 10. `notify` (placeholder)
 
 `notify` currently has optional notifier call behavior and no persisted pipeline
-outputs. The focused stage documents own implementation mechanics. The
+outputs; its default collaborator is a no-op sender. The focused stage
+documents own implementation mechanics. The
 [CLI](../cli.md) and [Operations](../operations.md) own user-visible invocation
 and execution semantics.
 
@@ -88,3 +89,8 @@ and execution semantics.
 
 Use this map to find an owner, then read its focused documentation and tests
 before changing behavior.
+
+The stage registry is implemented in `internal/stage/placeholders.go` and its
+ordering is protected by `internal/app/planner_test.go`. Cross-invocation skip,
+force, failure, and invalidation behavior is exercised in
+`internal/app/runner_test.go` and `internal/app/run_stage_test.go`.

docs/internal/stage-analyze.md

@@ -1,24 +1,29 @@
 # Stage: analyze
 
 ## Purpose
+
 Execute selected configured Scriptorium artifacts in dependency order and materialize outputs.
 
 ## Inputs
+
 - configured artifacts from `pipeline.scriptorium.artifacts`
-- optional selected artifact filter (`--artifacts`)
+- optional selected artifact keys supplied through the stage environment
 - built-in/configured/previous-session source references in artifact inputs
 
 Supported source families:
 - built-ins: `narratio.transcript.*`, `narratio.bounds.session`
-- prepared stable inputs: `narratio.input.players`, `narratio.input.party`, `narratio.input.glossary`
+- prepared stable inputs: `narratio.input.players`, `narratio.input.party`,
+  `narratio.input.glossary`
 - configured artifacts: `narratio.artifact.<key>`
 - previous-session cache: `narratio.previous_session.artifact.<key>`
 
 ## Outputs
+
 - one materialized output per executed configured artifact (`output_path`)
 - stage metadata describing selected/generated/reused artifacts
 
 ## Key Behavior
+
 - skips with metadata when Scriptorium config is missing or no executable artifacts remain.
 - builds runtime artifact catalog (built-ins + configured artifacts).
 - marks non-executable configured artifacts as reusable when output files already exist.
@@ -30,13 +35,26 @@ Supported source families:
 - validates non-empty output files and materializes canonical outputs.
 
 ## Failure Semantics
+
 - required missing configured/previous-session inputs fail.
 - missing required prepared stable input source includes prepare rerun guidance.
 - missing required previous-session source includes prepare rerun guidance.
-- missing required `narratio.transcript.final_markdown` or `narratio.transcript.final_trimmed_markdown` inputs includes render rerun guidance.
+- missing required `narratio.transcript.final_markdown` or
+  `narratio.transcript.final_trimmed_markdown` inputs includes render rerun
+  guidance.
 - dependency cycles or unavailable required dependencies fail.
 - adapter validation failures fail stage.
 
 ## Invariants
+
 - `analyze` performs no remote storage calls for previous-session source resolution.
 - output provenance and metadata are deterministic per execution.
+
+## Related Contracts And Tests
+
+- [Configuration](../config.md#scriptorium-artifact-entries) owns artifact
+  fields and source-selection rules.
+- [CLI](../cli.md) owns user-visible artifact selection.
+- [Scriptorium](../integrations/scriptorium.md) owns the subprocess contract.
+- Implementation and tests: `internal/stage/analyze.go`,
+  `internal/stage/analyze_test.go`

docs/internal/stage-merge.md

@@ -1,18 +1,22 @@
 # Stage: merge
 
 ## Purpose
+
 Normalize raw transcript inputs and merge into base transcript via Seriatim.
 
 ## Inputs
+
 - `transcripts/raw/*.json`
 - `inputs/speakers.yml`
 - `inputs/autocorrect.yml`
 
 ## Outputs
+
 - `transcripts/base.json`
 - optional `artifacts/seriatim.report.json`
 
 ## Key Behavior
+
 - discovers and validates raw transcript inputs.
 - normalizes each raw transcript (`seriatim.Normalize`) into run-local scratch output.
 - merges normalized inputs (`seriatim.Run`) into base transcript.
@@ -20,6 +24,14 @@ Normalize raw transcript inputs and merge into base transcript via Seriatim.
 - materializes canonical outputs and records stage logs/generated configs.
 
 ## Invariants
+
 - merge always consumes normalized forms of raw inputs.
 - base transcript must validate before stage success.
 - report output is config-gated.
+
+## Related Contracts And Tests
+
+- [Seriatim](../integrations/seriatim.md) owns subprocess and output semantics.
+- [Configuration](../config.md#pipeline) owns operator-selected Seriatim values.
+- Implementation and tests: `internal/stage/merge.go`,
+  `internal/stage/merge_test.go`

docs/internal/stage-normalize.md

@@ -1,16 +1,20 @@
 # Stage: normalize
 
 ## Purpose
+
 Normalize polished transcript into final transcript using Seriatim.
 
 ## Inputs
+
 - `transcripts/polished.json`
 
 ## Outputs
+
 - `transcripts/final.json` (or configured normalize output path)
 - optional `artifacts/seriatim.normalize.report.json`
 
 ## Key Behavior
+
 - resolves polished transcript from manifest outputs/canonical fallback.
 - applies `pipeline.normalize` config or default normalize config.
 - runs Seriatim normalize with configured timeout/binary.
@@ -18,5 +22,13 @@ Normalize polished transcript into final transcript using Seriatim.
 - materializes canonical outputs and records logs/generated configs.
 
 ## Invariants
+
 - final transcript must validate as processed transcript JSON (`segments` array).
 - normalize defaults are applied when `pipeline.normalize` is unset.
+
+## Related Contracts And Tests
+
+- [Seriatim](../integrations/seriatim.md) owns subprocess and output semantics.
+- [Configuration](../config.md#pipeline) owns normalize fields and defaults.
+- Implementation and tests: `internal/stage/normalize.go`,
+  `internal/stage/normalize_test.go`

docs/internal/stage-polish.md

@@ -1,17 +1,21 @@
 # Stage: polish
 
 ## Purpose
+
 Run Audita polishing on base transcript and produce polished transcript.
 
 ## Inputs
+
 - `transcripts/base.json`
 - `inputs/glossary.yml`
 
 ## Outputs
+
 - `transcripts/polished.json`
 - optional `artifacts/audita.report.json`
 
 ## Key Behavior
+
 - resolves base transcript from merge outputs/canonical fallback.
 - invokes Audita with configured model/module/runtime options.
 - validates processed transcript structure (`segments` array required).
@@ -19,5 +23,14 @@ Run Audita polishing on base transcript and produce polished transcript.
 - materializes canonical outputs; records logs/generated config and adapter metadata.
 
 ## Invariants
+
 - polished transcript schema validation is mandatory.
 - report output is config-gated.
+
+## Related Contracts And Tests
+
+- [Audita](../integrations/audita.md) owns subprocess, validation, and failure
+  semantics.
+- [Configuration](../config.md#pipeline) owns operator-selected Audita values.
+- Implementation and tests: `internal/stage/polish.go`,
+  `internal/stage/polish_test.go`

docs/internal/stage-prepare.md

@@ -1,17 +1,18 @@
 # Stage: prepare
 
 ## Purpose
+
 Materialize canonical current-session inputs before processing stages.
 
 ## Inputs
-- resolved `campaign.yml`, `session.yml`, and pipeline config
+
+- resolved campaign, session, and pipeline configuration
 - stable input files (`speakers`, `autocorrect`, `glossary`, `players`, `party`)
-- audio source:
-  - local `audio_dir`/`audio_files`, or
-  - S3 `audio_s3.prefix`
+- one resolved local or S3 audio source
 - enabled configured artifact input requirements for previous-session sources
 
 ## Outputs
+
 - `inputs/campaign.yml`
 - `inputs/session.yml`
 - `inputs/pipeline.resolved.yml`
@@ -26,6 +27,7 @@ Materialize canonical current-session inputs before processing stages.
 - deterministic `manifest.inputs` entries (checksums + provenance)
 
 ## Key Behavior
+
 - validates required config/store state.
 - enforces local audio vs S3 audio mutual exclusivity.
 - materializes S3 audio through spool/cache-aware logic.
@@ -39,6 +41,20 @@ Materialize canonical current-session inputs before processing stages.
 Required previous-session inputs fail when unavailable; optional missing inputs are skipped.
 
 ## Invariants
+
 - only `prepare` hydrates canonical `previous/` cache state.
-- managed previous artifacts are stored under `previous/artifacts/**` without duplicate `artifacts/artifacts/` nesting.
+- managed previous artifacts are stored under `previous/artifacts/**` without
+  duplicate `artifacts/artifacts/` nesting.
 - `manifest.inputs` ordering is deterministic (`kind`, `path`).
+
+## Related Contracts And Tests
+
+- [Configuration](../config.md) owns audio selection, stable input fields, and
+  previous-session settings.
+- [Operations](../operations.md) owns physical input, audio, spool, cache, and
+  previous-state layout.
+- [Storage Internals](storage.md) and [Artifact Internals](artifacts.md) explain
+  the internal collaborators.
+- Implementation and tests: `internal/stage/prepare.go`,
+  `internal/stage/prepare_test.go`, `internal/audio/s3_audio_test.go`,
+  `internal/previouscache/*_test.go`

docs/internal/stage-publish.md

@@ -1,23 +1,29 @@
 # Stage: publish
 
 ## Purpose
+
 Upload run/session outputs to object storage and atomically advance remote current state.
 
 ## Inputs
-- successful prerequisite stages: `prepare`, `transcribe`, `merge`, `polish`, `normalize`, `trim`, `render`, `analyze`
-- run root `runs/{run_id}/**`
-- publish output rules (`pipeline.publish.outputs`)
+
+- successful preceding stages from the [canonical stage set](overview.md#pipeline-stage-set)
+- invocation-scoped run files
+- resolved publish output rules
 - effective publish locks (static + remote merged lock set)
-- local `previous/**` files when present
+- durable previous-session cache files when present
 
 ## Outputs
-- uploaded run files under remote `runs/{run_id}/...` (excluding `audio/**`)
-- uploaded selected publish outputs under session prefix
-- uploaded `previous/**` files under session prefix when present
-- uploaded `current/manifest.json`
-- uploaded `current/run_id.txt` written last
+
+- uploaded invocation record and selected publish outputs;
+- uploaded durable previous-session cache files when present;
+- updated remote current manifest; and
+- remote current-run commit marker, written last.
+
+Exact remote placement and the operator workflow belong in
+[Operations](../operations.md#publish-workflow).
 
 ## Key Behavior
+
 - stage can self-skip when publish disabled or run upload disabled.
 - validates prerequisite stage success and object-store availability.
 - collects deterministic run file list plus run `manifest.json`.
@@ -28,6 +34,7 @@ Upload run/session outputs to object storage and atomically advance remote curre
 - writes remote current manifest before current run pointer.
 
 ## Metadata Signals
+
 Includes counts/lists for:
 - run uploads
 - published output uploads
@@ -39,6 +46,22 @@ Includes counts/lists for:
 - `current_pointer_written`
 
 ## Invariants
+
 - `current/run_id.txt` is the remote commit marker and is written last.
 - run upload excludes `audio/**`.
 - publish locks are not overridden by `--force`.
+
+The commit boundary and cleanup gate are normative architecture invariants; see
+[Architecture](../policy/architecture.md#publish-commit-boundary).
+
+## Related Contracts And Tests
+
+- [Configuration](../config.md#publish-configuration-summary) owns output and
+  static-lock fields.
+- [Operations](../operations.md#publish-locks) owns remote lock lifecycle and
+  physical remote state.
+- [Artifact Internals](artifacts.md) explains source resolution and current-state
+  helpers.
+- Implementation and tests: `internal/stage/publish.go`,
+  `internal/stage/publish_test.go`, `internal/app/operator_helpers_test.go`,
+  `internal/app/post_publish_cleanup_test.go`

docs/internal/stage-render.md

@@ -1,17 +1,21 @@
 # Stage: render
 
 ## Purpose
+
 Render Markdown transcript artifacts from normalized JSON transcripts via Seriatim.
 
 ## Inputs
+
 - `narratio.transcript.final` (`transcripts/final.json`)
 - `narratio.transcript.final_trimmed` (`transcripts/final.trimmed.json`)
 
 ## Outputs
+
 - `narratio.transcript.final_markdown` -> `transcripts/final.md`
 - `narratio.transcript.final_trimmed_markdown` -> `transcripts/final.trimmed.md`
 
 ## Key Behavior
+
 - uses `pipeline.render` settings (enabled/format/title/booleans).
 - resolves inputs manifest-first, then canonical fallback.
 - writes run-local outputs first, then materializes canonical session outputs.
@@ -19,11 +23,20 @@ Render Markdown transcript artifacts from normalized JSON transcripts via Seriat
 - skips with stage metadata when `pipeline.render.enabled=false`.
 
 ## Failure Semantics
+
 - missing normalized input fails with normalize rerun guidance.
 - missing trimmed input fails with trim rerun guidance.
 - adapter/subprocess failure fails stage.
 - empty render output files fail validation.
 
 ## Invariants
+
 - only `format: markdown` is supported.
 - render stage owns production of built-in Markdown transcript sources.
+
+## Related Contracts And Tests
+
+- [Seriatim](../integrations/seriatim.md) owns render subprocess behavior.
+- [Configuration](../config.md#pipeline) owns render fields and defaults.
+- Implementation and tests: `internal/stage/render.go`,
+  `internal/stage/render_test.go`

docs/internal/stage-transcribe.md

@@ -1,22 +1,36 @@
 # Stage: transcribe
 
 ## Purpose
+
 Generate raw per-speaker transcripts from prepared audio using WhisperX.
 
 ## Inputs
+
 - `audio/*.flac` from `prepare`
 
 ## Outputs
+
 - `transcripts/raw/<speaker>.json`
 
 ## Key Behavior
+
 - discovers prepared audio from manifest inputs or canonical audio directory.
 - derives speaker ID from `.flac` basename.
-- runs WhisperX with configured concurrency/retry settings.
+- dispatches WhisperX requests through a bounded worker pool.
 - validates each output as JSON.
 - writes run-local outputs then materializes canonical transcript outputs.
 
 ## Invariants
+
 - speaker basenames must be unique.
 - output path returned by adapter must match requested output path.
 - each successful output is validated before stage success.
+
+## Related Contracts And Tests
+
+- [WhisperX](../integrations/whisperx.md) owns HTTP, retry, timeout, and
+  cancellation semantics.
+- [Configuration](../config.md#pipeline) owns concurrency and other
+  operator-selected values.
+- Implementation and tests: `internal/stage/transcribe.go`,
+  `internal/stage/transcribe_test.go`

docs/internal/stage-trim.md

@@ -1,16 +1,21 @@
 # Stage: trim
 
 ## Purpose
-Produce a final-trimmed transcript. By default, the stage generates bounds and applies a bounds-driven trim.
+
+Produce a final-trimmed transcript. By default, the stage generates bounds and
+applies a bounds-driven trim.
 
 ## Inputs
+
 - `transcripts/final.json`
 
 ## Outputs
+
 - `transcripts/final.trimmed.json` (or configured trim output path)
 - when trim enabled: `artifacts/session_bounds.json`
 
 ## Key Behavior
+
 When `trim.enabled=true`:
 - runs Scriptorium bounds artifact generation;
 - optionally runs render-debug output generation;
@@ -23,6 +28,16 @@ When `trim.enabled=false`:
 - copies normalized transcript to trimmed output.
 
 ## Invariants
+
 - normalized transcript is required input.
 - bounds output exists only in enabled trim path.
 - render-debug output is diagnostic and not a declared stage output.
+
+## Related Contracts And Tests
+
+- [Scriptorium](../integrations/scriptorium.md) owns bounds generation and
+  debug-render subprocess behavior.
+- [Seriatim](../integrations/seriatim.md) owns transcript trimming behavior.
+- [Configuration](../config.md#pipeline) owns trim fields and defaults.
+- Implementation and tests: `internal/stage/trim.go`,
+  `internal/stage/trim_test.go`

docs/internal/storage.md

@@ -1,10 +1,16 @@
 # Internal: Storage
 
 ## Purpose
-Document remote object-store contracts and S3 implementation behavior.
+
+Explain the object-store interface and S3 implementation used by Narratio.
+Remote key layout and lifecycle belong in [Operations](../operations.md), while
+operator-selected storage fields and credential mechanisms belong in
+[Configuration](../config.md).
 
 ## Primary Contract
+
 `storage.ObjectStore` interface:
+
 - `List(ctx, prefix)`
 - `Download(ctx, key, localPath)`
 - `Upload(ctx, localPath, key, opts)`
@@ -14,15 +20,15 @@ Key invariant:
 - callers pass full bucket-relative keys;
 - storage implementations do not infer campaign/session/run prefixes.
 
-## Configuration
-`NewObjectStoreFromConfig` currently supports S3-backed stores from `pipeline.storage.*` config.
+## Composition
 
-S3 constructor behavior:
-- requires configured bucket;
-- uses region/endpoint/path-style options when set;
-- resolves credentials from configured env var names (with defaults).
+`NewObjectStoreFromConfig` constructs the S3-backed implementation from
+resolved configuration. The application loads configured filesystem secrets
+before calling it. The storage adapter consumes already-resolved values; it does
+not own discovery, defaults, or configuration validation.
 
 ## S3 Backend Behavior
+
 - normalizes object keys.
 - `List` paginates and returns normalized `ObjectInfo`.
 - `Download` writes local files with parent directory creation.
@@ -30,5 +36,13 @@ S3 constructor behavior:
 - `Exists` maps not-found responses to `false`.
 
 ## Invariants
+
 - storage layer is stateless regarding manifest/stage progression.
 - publish ordering semantics are owned by stage/app code, not storage adapters.
+
+## Implementation And Tests
+
+- Contract and S3 adapter: `internal/adapters/storage`
+- Composition: `internal/app/object_store.go`
+- Tests: `internal/adapters/storage/*_test.go`,
+  `internal/app/object_store_test.go`

docs/internal/workspace.md

@@ -1,57 +1,62 @@
 # Internal: Workspace
 
 ## Purpose
-Define local session layout, run-local stage layout, and cleanup guardrails.
 
-## Canonical Session Layout
-Session root:
-- `{workspace.root}/work/{campaign}/{session_id}`
+Explain the helpers that construct local session and run paths, coordinate
+single-writer access, and confine cleanup. The authoritative physical layout and
+retention workflow belong in [Operations](../operations.md#local-state-layout).
 
-Core directories/files:
-- `inputs/`
-- `audio/`
-- `transcripts/`
-- `artifacts/`
-- `reports/`
-- `logs/`
-- `config/`
-- `current/`
-- `runs/`
-- `previous/`
-- `manifest.json`
-- `.lock`
+## Path Ownership
 
-`previous/` reserved files:
-- `previous/manifest.json`
-- `previous/artifacts/**`
+`internal/artifacts` owns canonical session, run, spool, cache, and
+previous-cache path construction. `SessionPathsFor` provides the session-scoped
+path model, and layout creation goes through `EnsureLayoutFor`. Callers should
+consume those helpers instead of rebuilding relative paths.
+
+`internal/pathsafe` and application cleanup helpers enforce confinement for
+relative destinations and deletion targets.
 
 ## Run-Local Stage Layout
-When run context is available, stages use:
-- `runs/{run_id}/{stage}/outputs/`
-- `runs/{run_id}/{stage}/logs/`
-- `runs/{run_id}/{stage}/reports/`
-- `runs/{run_id}/{stage}/config/`
-- `runs/{run_id}/{stage}/scratch/`
 
-Run-local outputs are materialized back into canonical session paths before stage success.
-`previous/**` writes are never redirected to run-local output paths.
+`internal/stage/run_local.go` maps stage outputs and diagnostics into an
+invocation-scoped layout. Successful outputs are validated and atomically
+materialized into canonical session paths before stage success. Managed
+previous-session cache paths remain session-durable and are never redirected
+into run-local output space.
 
 ## Locking
-`artifacts.LocalStore` enforces single-writer session lock via `.lock` file (`ErrLockConflict` on contention).
+
+`artifacts.LocalStore` enforces the single-writer session lock via `.lock`
+(`ErrLockConflict` on contention).
 
 ## Cleanup Semantics
+
 Automatic post-publish cleanup:
+
 - only runs when publish actually executed and succeeded;
 - requires `uploaded=true` and `current_pointer_written=true` metadata;
-- respects `pipeline.spool.delete_audio_after_publish` and `pipeline.workspace.cleanup_after_publish`;
+- consumes the resolved cleanup policy described in
+  [Configuration](../config.md);
 - refuses unsafe deletes (root delete, out-of-root delete, symlink paths).
 
-Manual clean command:
-- `clean <session_id>` removes session work and spool subtree.
-- `clean --all` removes all workspace work and spool children.
-- durable cache is preserved unless `--clear-cache` is requested.
+Manual cleanup uses the same scoped-target checks. Invocation syntax and exact
+deletion scope belong in [CLI](../cli.md#clean) and
+[Operations](../operations.md#cleanup).
 
 ## Invariants
+
 - campaign-aware session root is mandatory.
 - manifest-driven stage state is durable across runs.
 - cleanup guardrails prevent destructive root/out-of-scope deletion.
+
+## Implementation And Tests
+
+- Path model and local store: `internal/artifacts/paths.go`,
+  `internal/artifacts/local.go`
+- Run-local materialization: `internal/stage/run_local.go`
+- Cleanup confinement: `internal/app/cleanup_targets.go`,
+  `internal/app/post_publish_cleanup.go`
+- Tests: `internal/artifacts/paths_model_test.go`,
+  `internal/artifacts/local_test.go`, `internal/stage/run_local_test.go`,
+  `internal/app/cleanup_targets_test.go`,
+  `internal/app/post_publish_cleanup_test.go`

docs/troubleshooting.md

@@ -66,7 +66,8 @@ narratio session plan 2026-04-04 --config /path/pipeline.yml --campaign-file /pa
 
 Safe fix:
 
-- align config with [docs/config.md](./config.md) and maintained files under `examples/`.
+- align config with [Configuration](./config.md) and the
+  [maintained examples](../examples/README.md).
 
 Relevant reference: [Configuration](./config.md).
 

examples/README.md

@@ -0,0 +1,46 @@
+# Maintained Examples
+
+These files are safe, copyable starting points for Narratio configuration and
+input structure. Replace placeholder identifiers, storage names, integration
+URLs, and paths for the target environment. Field meanings and defaults belong
+in the [configuration reference](../docs/config.md).
+
+## Pipeline Configuration
+
+- [Minimal pipeline](pipeline.minimal.yml): campaign discovery plus the required
+  WhisperX URL.
+- [Production-shaped pipeline](pipeline.production.yml): S3 storage, publish,
+  external tools, and configured Scriptorium artifacts.
+- [Full annotated pipeline](pipeline.full.annotated.yml): every implemented
+  pipeline section with explanatory comments.
+
+The existing `internal/config` example test loads and validates each pipeline
+with the sample campaign and a compatible local- or S3-audio session.
+
+## Campaign And Session Configuration
+
+- [Sample campaign](campaigns/sample-campaign/campaign.yml), its
+  [session template](campaigns/sample-campaign/session.template.yml), and its
+  adjacent stable inputs provide a complete campaign directory shape.
+- [Local-audio session](session.local-audio.yml) and
+  [S3-audio session](session.s3-audio.yml) are concrete session files.
+- [Session template](session.template.yml) and the campaign-local equivalent
+  demonstrate the narrow placeholder syntax consumed by `session init`; they
+  are templates, not runtime session files.
+
+## Input Fixtures
+
+- [Speakers](speakers.yml), [autocorrect](autocorrect.yml), and
+  [glossary](glossary.yml) show the standalone input shapes.
+- The sample campaign references its local
+  [speakers](campaigns/sample-campaign/speakers.yml),
+  [autocorrect](campaigns/sample-campaign/autocorrect.yml),
+  [glossary](campaigns/sample-campaign/glossary.yml),
+  [players](campaigns/sample-campaign/players.yml), and
+  [party](campaigns/sample-campaign/party.yml) fixtures.
+- [Sample speaker audio](audio/sample-speaker.flac) is a text placeholder that
+  reserves the expected filename and directory shape. Replace it with a real
+  FLAC file before running transcription.
+
+The examples contain environment-variable names but no credential values. They
+use fictional campaign content and reserved example domains.

examples/campaigns/sample-campaign/speakers.yml

@@ -1,5 +1,5 @@
 match:
-  - speaker: "Eric Rakestraw"
+  - speaker: "Example Speaker"
     match:
-      - "Eric_Rakestraw"
-      - "Eric"
+      - "Example_Speaker"
+      - "Example"

examples/speakers.yml

@@ -1,5 +1,5 @@
 match:
-  - speaker: "Eric Rakestraw"
+  - speaker: "Example Speaker"
     match:
-      - "Eric_Rakestraw"
-      - "Eric"
+      - "Example_Speaker"
+      - "Example"