Implement runner retries and raw validation

docs/config.md

@@ -228,8 +228,9 @@ Binding fields:
 - `module`: module key.
 - `llm_profile`: optional Scriptorium profile ID. Empty or omitted lets the
   Scriptorium prompt default select the profile.
-- `retries`: non-negative retry count for runtime stages that support retries.
-  The current runner preserves this value in resolved config.
+- `retries`: non-negative retry count for extra runtime attempts after the
+  first attempt. The runner applies retries to `chunk`, `extract`, `merge`, and
+  `normalize` bindings.
 - `options`: optional module-specific settings.
 - `references`: optional reference bindings. Supported only for `chunk`,
   `extract`, `merge`, and `normalize` bindings. `input`, validator, and

docs/integrations/json-output.md

@@ -96,8 +96,9 @@ stage, lane ID when present, slot name, origin type and URI, digest, media
 type, byte size, and binding source. Reference content is not written to
 durable output.
 
-Reference `stage` is `chunk`, `extract`, or `normalize`. `lane_id` is omitted
-for chunk references and present for extract and normalize references.
+Reference `stage` is `chunk`, `extract`, `merge`, or `normalize`. `lane_id` is
+omitted for chunk references and present for extract, merge, and normalize
+references.
 
 `validation_status` is `approved` when no raw outputs were rejected and
 `rejected` when one or more raw outputs were rejected.

docs/internal/pipeline.md

@@ -116,8 +116,9 @@ The runner:
 1. validates run input and registries;
 2. builds the input adapter and parses the raw input into a source document;
 3. validates the source document;
-4. builds the chunker and produces source chunks;
-5. validates source chunks against framework invariants;
+4. builds the chunker and produces source chunks, retrying when configured;
+5. validates source chunks against framework invariants and any registered raw
+   chunk validators;
 6. runs each selected artifact lane in sorted resolved order;
 7. builds the output encoder and validates logical output file names.
 
@@ -129,9 +130,8 @@ configured LLM profile, module options, and run metadata. Deterministic and
 LLM-backed chunkers use the same contract; provider construction stays outside
 chunk modules.
 
-After `Chunk` returns, the runner appends chunker warnings before returning any
-chunker error. When chunking succeeds, the runner validates generic chunk
-invariants before running extractors:
+When chunking succeeds, the runner validates generic chunk invariants before
+running extractors:
 
 - chunk IDs must be non-empty and unique in the chunk result;
 - each chunk `SourceID` must match the source document ID;
@@ -150,6 +150,10 @@ chunk metadata. Extractors and downstream stages therefore see canonical source
 units, while `SourceChunk.Metadata` remains the supported place for
 chunker-owned context.
 
+If chunk validation rejects a chunk after configured retries, the runner records
+a rejected raw output and skips downstream lane execution. Framework-level
+chunking or validation errors that remain after configured retries fail the run.
+
 The framework does not require complete source-unit coverage and does not reject
 overlap between different chunks. Stricter policies, such as full coverage or
 non-overlap, belong to individual chunk modules when they are part of that
@@ -159,24 +163,37 @@ Within an artifact lane, the runner:
 
 1. builds the extractor, merger, and normalizer;
 2. records module manifest metadata when modules provide it;
-3. extracts one raw `ExtractOutput` from each chunk;
+3. extracts one raw `ExtractOutput` from each accepted chunk, retrying when
+   configured;
 4. fills runner-owned provenance on each extract output, including lane ID,
    extractor key, source ID, chunk ID, and chunk index;
-5. merges ordered extract outputs into one raw `MergeOutput`;
-6. normalizes the merge output into one raw `NormalizeOutput`;
-7. appends the normalized raw output to `RunOutput.NormalizeOutputs`.
+5. validates raw extract outputs and omits rejected outputs from merge input;
+6. merges ordered accepted extract outputs into one raw `MergeOutput`, retrying
+   when configured;
+7. validates raw merge output and skips normalization for rejected merge output;
+8. normalizes the accepted merge output into one raw `NormalizeOutput`,
+   retrying when configured;
+9. validates raw normalize output and appends accepted normalized raw output to
+   `RunOutput.NormalizeOutputs`.
 
 ## Validators
 
 The current runner handoff is raw-output based. Extractors, mergers, and
 normalizers do not advertise candidate validator chains through their module
-interfaces. `RunOutput.Rejected` is reserved for rejected raw outputs when raw
-validation is wired into the runner.
+interfaces. Runner-side raw validation chains receive the raw module output plus
+stage, lane, module, source, and chunk provenance. Empty raw validation chains
+approve output by default.
+
+Validator rejection is a non-fatal run outcome: the rejected output is recorded
+in `RunOutput.Rejected` and does not pass to the next stage. Validator execution
+errors are framework-level errors and retry according to the relevant binding.
 
 ## Warnings And Failures
 
-Warnings from chunking, extraction, merging, normalization, and output encoding
-are accumulated in `RunOutput.Warnings`.
+Warnings from the successful chunking, extraction, merging, and normalization
+attempts whose outputs are used are accumulated in `RunOutput.Warnings`, along
+with output encoder warnings. Warnings from discarded retry attempts are not
+promoted to final warnings.
 
 Errors wrap the operation and module key or lane context. If execution fails
 after a manifest exists, the returned manifest is marked `failed` and receives a

docs/operations.md

@@ -133,7 +133,9 @@ There is no command to resume a failed run. Re-run `notarius run` after fixing
 the cause.
 
 Provider retries and timeouts are handled by Scriptorium according to the
-selected execution profile. There is no separate CLI retry command.
+selected execution profile. Pipeline module retries are controlled by module
+binding `retries` values in config for chunk, extract, merge, and normalize.
+There is no separate CLI retry command.
 
 Notarius writes local files only. Remote storage and archive management are not
 part of the implemented CLI.