subconscious: flatten agents/ nesting, move prompts in

agents/*.agent definitions and prompts/ now live under
src/subconscious/ alongside the code that uses them.
No more intermediate agents/ subdirectory.

Co-Authored-By: Proof of Concept <poc@bcachefs.org>

src/subconscious/mod.rs

@@ -1,7 +1,28 @@
-// subconscious — autonomous agents that process without being asked
+// Agent layer: LLM-powered operations on the memory graph
 //
-// Reflect, surface, consolidate, digest, audit — the background
-// processes that maintain and evolve the memory graph. Runs on
-// local models via the API backend.
+// Everything here calls external models (Sonnet, Haiku) or orchestrates
+// sequences of such calls. The core graph infrastructure (store, graph,
+// spectral, search, similarity) lives at the crate root.
+//
+//   llm          — model invocation, response parsing
+//   prompts      — prompt generation from store data
+//   defs         — agent file loading and placeholder resolution
+//   audit        — link quality review via Sonnet
+//   consolidate  — full consolidation pipeline
+//   knowledge    — agent execution, conversation fragment selection
+//   enrich       — journal enrichment, experience mining
+//   digest       — episodic digest generation (daily/weekly/monthly)
+//   daemon       — background job scheduler
+//   transcript   — shared JSONL transcript parsing
 
-pub mod agents;
+pub mod transcript;
+pub mod api;
+pub mod llm;
+pub mod prompts;
+pub mod defs;
+pub mod audit;
+pub mod consolidate;
+pub mod knowledge;
+pub mod enrich;
+pub mod digest;
+pub mod daemon;