Finish Scriptorium runtime documentation

docs/internal/pipeline.md

@@ -23,7 +23,8 @@ before execution:
    - merge: `appendorder`
    - normalize: `noop`
    - output: `json`
-   - LLM profile: `default`
+   - LLM profile: empty, which lets Scriptorium prompt defaults choose a
+     profile.
 4. The module catalog is checked for each bound module key.
 5. Module capabilities are checked in workflow order.
 6. A digest is calculated from the resolved pipeline without the digest field.
@@ -54,13 +55,19 @@ empty bound files. Media-type acceptance is checked only when a slot declares
 manifests. The CLI writes provenance-only resolved reference diagnostics, and
 the run manifest records target-stage reference provenance separately from
 source digests. Runtime reference content is passed to the matching chunker,
-extractor, or normalizer request.
+extractor, or normalizer request. LLM-backed modules pass that material onward
+as named Scriptorium prompt inputs.
 
-Prompt bundles can declare reference slots and use `reference` and
-`hasreference` template functions. Bundle loading validates string-literal slot
-names against the declaration. Rendering receives a target reference set from the
-caller; unbound optional slots render as empty strings, and `hasreference`
-returns true only when at least one bound item has content.
+The CLI carries raw input bytes into `pipeline.RunInput`. Input adapters parse
+those bytes into the source document, while LLM-backed modules that need the
+original transcript material can pass the same bytes as a prompt input with
+origin metadata. The raw input payload is not written to manifests or default
+diagnostics.
+
+The CLI also carries an optional run `session_id`. The runner makes it available
+to chunk, extract, and normalize requests; LLM-backed modules forward it through
+their structured completion requests so Scriptorium can include it in prompt
+execution metadata.
 
 ## Registries And Module Specs