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/llm.rs

@@ -0,0 +1,73 @@
+// LLM utilities: model invocation via direct API
+
+use crate::store::Store;
+
+use regex::Regex;
+use std::fs;
+
+/// Simple LLM call for non-agent uses (audit, digest, compare).
+/// Logs to llm-logs/{caller}/ file.
+pub(crate) fn call_simple(caller: &str, prompt: &str) -> Result<String, String> {
+    let log_dir = crate::store::memory_dir().join("llm-logs").join(caller);
+    fs::create_dir_all(&log_dir).ok();
+    let log_path = log_dir.join(format!("{}.txt", crate::store::compact_timestamp()));
+
+    use std::io::Write;
+    let log = move |msg: &str| {
+        if let Ok(mut f) = fs::OpenOptions::new()
+            .create(true).append(true).open(&log_path)
+        {
+            let _ = writeln!(f, "{}", msg);
+        }
+    };
+
+    super::api::call_api_with_tools_sync(caller, prompt, None, &log)
+}
+
+/// Call a model using an agent definition's configuration.
+pub(crate) fn call_for_def(
+    def: &super::defs::AgentDef,
+    prompt: &str,
+    log: &(dyn Fn(&str) + Sync),
+) -> Result<String, String> {
+    super::api::call_api_with_tools_sync(&def.agent, prompt, def.temperature, log)
+}
+
+/// Parse a JSON response, handling markdown fences.
+pub(crate) fn parse_json_response(response: &str) -> Result<serde_json::Value, String> {
+    let cleaned = response.trim();
+    let cleaned = cleaned.strip_prefix("```json").unwrap_or(cleaned);
+    let cleaned = cleaned.strip_prefix("```").unwrap_or(cleaned);
+    let cleaned = cleaned.strip_suffix("```").unwrap_or(cleaned);
+    let cleaned = cleaned.trim();
+
+    if let Ok(v) = serde_json::from_str(cleaned) {
+        return Ok(v);
+    }
+
+    // Try to find JSON object or array
+    let re_obj = Regex::new(r"\{[\s\S]*\}").unwrap();
+    let re_arr = Regex::new(r"\[[\s\S]*\]").unwrap();
+
+    if let Some(m) = re_obj.find(cleaned)
+        && let Ok(v) = serde_json::from_str(m.as_str()) {
+            return Ok(v);
+        }
+    if let Some(m) = re_arr.find(cleaned)
+        && let Ok(v) = serde_json::from_str(m.as_str()) {
+            return Ok(v);
+        }
+
+    let preview = crate::util::first_n_chars(cleaned, 200);
+    Err(format!("no valid JSON in response: {preview}..."))
+}
+
+/// Get all keys for prompt context.
+pub(crate) fn semantic_keys(store: &Store) -> Vec<String> {
+    let mut keys: Vec<String> = store.nodes.keys()
+        .cloned()
+        .collect();
+    keys.sort();
+    keys.truncate(200);
+    keys
+}