agents: phase tracking, pid files, pipelining, unified cycle

- AgentStep with phase labels (=== PROMPT phase:name ===)
- PID files in state dir (pid-{PID} with JSON phase/timestamp)
- Built-in bail check: between steps, bail if other pid files exist
- surface_observe_cycle replaces surface_agent_cycle + journal_agent_cycle
- Reads surface output from state dir instead of parsing stdout
- Pipelining: starts new agent if running one is past surface phase
- link_set upserts (creates link if missing)
- Better error message for context window overflow

Co-Authored-By: Kent Overstreet <kent.overstreet@linux.dev>

src/subconscious/prompts.rs

@@ -12,9 +12,14 @@ use crate::neuro::{
 /// Result of building an agent prompt — includes both the prompt text
 /// and the keys of nodes selected for processing, so the caller can
 /// record visits after successful completion.
+/// A resolved step ready for execution.
+pub struct ResolvedStep {
+    pub prompt: String,
+    pub phase: String,
+}
+
 pub struct AgentBatch {
-    /// Prompt steps — single-step agents have one entry, multi-step have several.
-    pub prompts: Vec<String>,
+    pub steps: Vec<ResolvedStep>,
     pub node_keys: Vec<String>,
 }
 
@@ -364,7 +369,7 @@ pub fn split_plan_prompt(store: &Store, key: &str) -> Result<String, String> {
     let graph = store.build_graph();
     // Override the query — we have a specific key to split
     let keys = vec![key.to_string()];
-    let template = def.prompts.first().ok_or_else(|| "split.agent has no prompts".to_string())?;
+    let template = def.steps.first().map(|s| &s.prompt).ok_or_else(|| "split.agent has no steps".to_string())?;
     let (prompt, _) = super::defs::resolve_placeholders(template, store, &graph, &keys, 1);
     Ok(prompt)
 }
@@ -386,11 +391,11 @@ pub fn split_extract_prompt(store: &Store, parent_key: &str, child_key: &str, ch
 pub fn consolidation_batch(store: &Store, count: usize, auto: bool) -> Result<(), String> {
     if auto {
         let batch = agent_prompt(store, "replay", count)?;
-        for (i, p) in batch.prompts.iter().enumerate() {
-            if batch.prompts.len() > 1 {
-                println!("=== STEP {} ===\n", i + 1);
+        for (i, s) in batch.steps.iter().enumerate() {
+            if batch.steps.len() > 1 {
+                println!("=== STEP {} ({}) ===\n", i + 1, s.phase);
             }
-            println!("{}", p);
+            println!("{}", s.prompt);
         }
         return Ok(());
     }