v0.21.0: agent reliability overhaul — plan integrity, target validation, observability pipelines, learning loop

P0 — stop the bleeding:
- prevent premature complete_task(success) when goal involves reachability
- validate run targets: block host-only commands (qm/pct/pvesh) on LXC/VM
- bump MCP client timeout 30s→120s to stop 'context deadline exceeded'

P1 — fix the plan system:
- add replaced_reason column to session_plan_steps (migration 030)
- track WHY steps are replaced (wrong_diagnosis/scope_change/superseded/etc)
- force fresh propose_plan on session resume (reopenSession marks old plan)

P2 — cognitive guardrails:
- SOUL.md scope-gate rule: ask before chasing unrelated subsystems
- auto-upsert knowledge entry on every session close

P3 — observability (all were empty/NULL):
- populate agent_activity.token_count from LLM usage (was always NULL)
- populate nomos_plan_executions linking executions to sessions
- write plan_completion_rate metric on task close

P4 — learning loop (all were empty/NULL):
- auto-classify every run call → classifications table (was 0 rows)
- auto-feedback on session close (was 0 rows)

cmd/nomos/agent.go

@@ -382,7 +382,12 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 		var msg openai.ChatCompletionMessage
 		var acc openai.ChatCompletionAccumulator
 
-		for attempt := 0; attempt <= maxLLMRetries; attempt++ {
+		// Capture token usage from this LLM response for activity logging.
+	// Previously always NULL — every agent_activity row had no token
+	// count. Now each tool call in this iteration gets the same total.
+	totalTokens := 0
+
+	for attempt := 0; attempt <= maxLLMRetries; attempt++ {
 			acc = openai.ChatCompletionAccumulator{}
 			stream := a.provider.Chat.Completions.NewStreaming(ctx, params, a.reqOpts...)
 			for stream.Next() {
@@ -414,14 +419,19 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 			msg = acc.Choices[0].Message
 			finishReason := acc.Choices[0].FinishReason
 
+			// Capture token usage from this iteration.
+			if acc.Usage.TotalTokens > 0 {
+				totalTokens = int(acc.Usage.TotalTokens)
+			}
+
 			if len(msg.ToolCalls) == 0 {
 				if isRefusalOrEmpty(msg.Content) {
-					if attempt < maxLLMRetries {
-						slog.Warn("nomos: empty or refusal response, retrying",
-							"session", sessionID, "iter", i+1, "attempt", attempt+1,
-							"content_len", len(msg.Content), "finish_reason", finishReason)
-						continue
-					}
+				if attempt < maxLLMRetries {
+					slog.Warn("nomos: empty or refusal response, retrying",
+						"session", sessionID, "iter", i+1, "attempt", attempt+1,
+						"content_len", len(msg.Content), "finish_reason", finishReason)
+					continue
+				}
 					// B.4: surface the real error context (finish_reason +
 					// refusal text) instead of a generic "empty response" —
 					// the operator can tell "content_filter — rephrase" from
@@ -505,7 +515,7 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 					slog.Warn("nomos: run retry cap hit — refusing dispatch",
 						"target", t, "failures", n, "session", sessionID)
 					a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args,
-						tc.Function.Arguments, directive, 0, false, correlationID)
+						tc.Function.Arguments, directive, 0, false, correlationID, totalTokens)
 					emit(agentEvent{
 						Type:      "tool_result",
 						Data:      map[string]any{"name": tc.Function.Name, "result": directive, "id": tc.ID, "retry_capped": true},
@@ -556,7 +566,7 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 			inputStr := string(inputJSON)
 
 			if callErr != nil {
-				a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, callErr.Error(), elapsed, false, correlationID)
+				a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, callErr.Error(), elapsed, false, correlationID, totalTokens)
 
 				// Retry cap: dispatch errors (e.g. MCP client timeout)
 				// count toward the cap too. A command that keeps timing
@@ -586,7 +596,7 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 			}
 
 			resultJSON, _ := json.Marshal(result)
-			a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, string(resultJSON), elapsed, true, correlationID)
+			a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, string(resultJSON), elapsed, true, correlationID, totalTokens)
 
 			// Link any execution this tool queued/started back to this
 			// session, so the auto-continuation worker can feed its result