Verify the integrated application and complete the migration

docs/integrations/output-files.md

@@ -9,7 +9,7 @@ the [CLI](../cli.md#streams-and-exit-status).
 
 ## Corrected Transcript
 
-The [output setting](../config.md#pipeline-and-output) selects the envelope:
+The [output setting](../config.md#settings) selects the envelope:
 
 | Encoder | JSON shape |
 | --- | --- |

docs/integrations/transcript-glossary-files.md

@@ -42,7 +42,7 @@ The top-level object contains a `glossary` list with at least one entry.
 
 The parser checks empty strings without trimming them. Unknown YAML fields are
 ignored by the glossary parser, unlike the stricter
-[configuration-file schema](../config.md#file-schema).
+[configuration-file schema](../config.md#loading-and-precedence).
 
 The [tiny glossary](../../examples/tiny-glossary.yaml) is a complete copyable input.
 Malformed YAML, an empty/missing glossary, invalid shapes, missing required text,

docs/internal/diagnostics-reporting.md

@@ -75,5 +75,4 @@ Operational handling of transcript-bearing artifacts belongs to
 - `internal/core/diagnostics/*_test.go`
 - `internal/framework/processreport/*_test.go`
 - `internal/core/reporting/report_test.go`
-- `internal/cli/run_test.go`
 - `cmd/audita/main_integration_test.go`

docs/internal/modules.md

@@ -3,7 +3,7 @@
 ## Scope
 
 This document covers internal module contracts and packages. User-selectable keys
-and the default sequence belong to [configuration](../config.md#pipeline-and-output).
+and the default sequence belong to [configuration](../config.md#settings).
 
 ## Module Contract
 

docs/internal/output-schemas.md

@@ -6,7 +6,7 @@
 JSON envelopes and segment fields are defined by the
 [output-file contract](../integrations/output-files.md#corrected-transcript);
 selectable values and defaults belong to
-[configuration](../config.md#pipeline-and-output).
+[configuration](../config.md#settings).
 
 ## Resolution and Encoding
 

docs/internal/pipeline.md

@@ -63,5 +63,4 @@ reports are derived from actual run results. Global requirements are owned by th
 
 - `internal/framework/runner/runner_test.go`
 - `internal/framework/proposal_generation/*_test.go`
-- `internal/cli/run_test.go`
 - `cmd/audita/main_integration_test.go`

docs/internal/validators.md

@@ -4,7 +4,7 @@
 
 This document describes internal validator composition, execution order, and
 decision handling. These registry keys identify implementation components; they
-are not independently selectable through [configuration](../config.md#pipeline-and-output).
+are not independently selectable through [configuration](../config.md#settings).
 
 ## Ownership
 

docs/operations.md

@@ -37,7 +37,7 @@ output files elsewhere.
 
 ## Diagnostics Directory
 
-The [diagnostics configuration](config.md#thresholds-context-and-diagnostics)
+The [diagnostics configuration](config.md#settings)
 selects the parent work directory. Runs create children named like
 `run-<unix-nanoseconds>`. The runtime creates the work directory if needed.
 Report paths may be relative when the supplied work directory is relative;
@@ -68,7 +68,7 @@ write succeeded or that the files still exist after retention.
 
 ## Retention Behavior
 
-[Configuration](config.md#thresholds-context-and-diagnostics) owns accepted
+[Configuration](config.md#settings) owns accepted
 retention values and the default. Current lifecycle behavior is:
 
 | Run outcome / selection | Directory outcome |
@@ -89,10 +89,10 @@ Run artifacts can contain full transcripts, glossary-related context, and LLM
 prompts/responses. Configured-key redaction does not anonymize those contents.
 Choose a work directory whose ownership and permissions fit the transcript data,
 and retain or share artifacts intentionally. Credential-supply mechanisms are
-owned by [configuration](config.md#secrets).
+owned by [configuration](config.md#credentials).
 
 For a debugging run, select retained diagnostics using the
-[retention flag](cli.md#process-flag-reference). Copy needed artifacts before
+[retention flag](cli.md#setting-overrides). Copy needed artifacts before
 removing completed run directories manually. Avoid deleting a directory while
 its run is active. Audita does not provide a separate archival/backup or remote
 artifact storage facility.

docs/roadmap/configkit.md

@@ -2,9 +2,9 @@
 
 **Last updated:** 2026-09-24
 
-**Status:** Final target selected; production implementation pending. The boundary
-and selected overlays are verified. The [implementation plan](implementation.md)
-owns execution stages; no production migration or release has begun.
+**Status:** Production implementation complete. The selected configuration and
+overlay model is implemented; [implementation evidence](implementation.md)
+records verification. No release has been published.
 
 ## Purpose and Direction
 
@@ -20,15 +20,14 @@ guide instead of legacy loaders, aliases, dual operating modes, or an ongoing
 compatibility layer. Retain existing syntax only when it independently suits the
 new model, not because compatibility requires it.
 
-The initial review and prototype used ConfigKit v0.3.1. The prototype now pins
-v0.4.0 and verifies its selected-overlay path; original v0.3.1 findings remain
-historical. The installed
-application must depend on a versioned module, not a sibling checkout or local
-module replacement.
+The initial review and prototype used ConfigKit v0.3.1, then verified v0.4.0
+selected overlays. Those findings remain historical; the prototype was removed
+after production integration. The application depends on a versioned module,
+without a sibling checkout or local module replacement.
 
 The shared boundary/prototype unit is complete. Its [selected contract, inventory,
 and evidence](library-boundary-findings.md) define the detailed target alongside
-this roadmap. Production configuration migration has not begun.
+this roadmap. Production configuration migration is complete.
 
 ## Target End State
 

docs/roadmap/implementation.md

@@ -2,7 +2,7 @@
 
 **Last updated:** 2026-09-24
 
-**Status:** Ready for implementation. All stages below are pending. This replaces
+**Status:** Implemented. All twelve stages are complete. This replaced
 the completed testing-overlay prototype plan; its results remain in the
 [boundary findings](library-boundary-findings.md#selected-overlay-extension-2026-09-24).
 
@@ -583,7 +583,21 @@ belongs to Stage 12.
 
 ## Stage 12: Verify the Combined Application and Close the Refactor
 
-**Status:** Pending. **Depends on:** Stages 1–11.
+**Status:** Complete. Controlled HTTP subprocess tests passed for base and testing
+overlay selection, explicit validation-profile and domain overrides, both outbound
+models, accepted repair, domain rejection without semantic retry, warning-only
+repair exhaustion, empty and repeated module pipelines, and safe partial failure
+diagnostics. `go test ./...`, `go build -o ./bin/audita ./cmd/audita`, focused
+race tests for runtime/runner/subprocess code, and both Linux release builds
+passed. The full suite also passed under Go 1.25.5 with offline module access.
+Maintained examples and local documentation links validated; `git diff --check`
+passed. No native macOS or live provider call was run. Release preparation remains
+separate: propose Audita v2.0.0 with [one migration guide](../migrations/v2.md),
+the actual pinned production dependency/license inventory, and LGPL
+notice/source/rebuild-distribution review before publication. No release was
+published here.
+
+**Depends on:** Stages 1–11.
 **Owns:** final integration tests, final defect fixes within this scope, and status/evidence.
 
 1. Complete representative production subprocess workflows against controlled HTTP:

docs/roadmap/library-adoption.md

@@ -2,10 +2,9 @@
 
 **Last updated:** 2026-09-24
 
-**Status:** Final target selected; production implementation pending. The shared
-boundary and offline prototype, including ConfigKit v0.4.0 overlays, are verified.
-[Implementation stages](implementation.md) are owned by the implementation plan.
-This roadmap defines the end state and user intent; it authorizes no publication.
+**Status:** Production implementation complete. ConfigKit v0.4.0 and PromptKit
+v0.11.0 are adopted; [implementation evidence](implementation.md) records the
+completed checks. Release compliance and publication remain separate work.
 
 ## Goal and Ownership