fix(cli): batch UX improvements for CLI help and feedback

- --reanalyze flag: add default hint (only unanalyzed files)
- do-update: add next-step hint when analyze=true
- list-databases --delete: warn that analysis data is lost
- watch --concurrency: use specific description, not shared flag
- introspect epilog: correct target default from examples to all
- ask --continue-from: add placement guidance
- benchmark canary warning: use [CANARY WARNING] prefix
- benchmark pre-run: show mode (fast/full/no-judge) in log
- benchmark checkpoint error: show (changed) not raw hashes, add recovery hint
- benchmark --resume: detect when path is consumed as checkpoint ID
- benchmark cost warning: standardize to [COST WARNING] prefix

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: leifericf

src/noumenon/benchmark.clj

@@ -1026,8 +1026,8 @@
         cost-ans (llm/estimate-cost model est-in est-out)
         cost-jdg (llm/estimate-cost (or judge-model model) est-in est-out)
         total    (+ cost-ans cost-jdg)]
-    (log! (str "WARNING: Benchmarks are expensive. "
-               total-stages " stages × ~"
+    (log! (str "[COST WARNING] Benchmarks are expensive. "
+               total-stages " stages x ~"
                (:input avg-tokens-per-stage) " input + ~"
                (:output avg-tokens-per-stage) " output tokens/stage"))
     (when (pos? total)
@@ -1201,7 +1201,7 @@
                    " run-id=" run-id
                    " details=" (pr-str (:details eval-result))))
         (when (= :warn (:status eval-result))
-          (log! "WARNING: All canary questions scored :wrong. Results may be unreliable — check model/provider configuration."))))
+          (log! "[CANARY WARNING] All canary questions failed — results may be unreliable. Check that analyze has been run and the correct model is configured."))))
 
     (when-not @stop-flag
       (run-pairs! rest-pairs shared concurrency))))
@@ -1480,6 +1480,10 @@
                " questions=" (count questions)
                " layers=" (str/join "," (map name layers))
                " stages=" total
+               " mode=" (cond
+                          (:deterministic-only mode) "fast"
+                          (:skip-judge mode)         "no-judge"
+                          :else                      "full")
                (when (:skip-judge mode) " skip-judge")
                (when (:deterministic-only mode) " deterministic-only")
                (when resuming?

src/noumenon/cli.clj

@@ -113,7 +113,7 @@
 
 (def ^:private reanalyze-flag
   {:flag "--reanalyze" :key :reanalyze :parse :string
-   :desc "Re-analyze files: all, prompt-changed, model-changed, stale"
+   :desc "Re-analyze files: all, prompt-changed, model-changed, stale (default: only unanalyzed files)"
    :error-missing :missing-reanalyze-value})
 
 (def ^:private analyze-flags
@@ -150,7 +150,10 @@
             :desc "Also run LLM analysis on changed files"}
            model-flag
            (assoc provider-flag :valid all-valid-providers)
-           db-dir-flag concurrency-flag]
+           db-dir-flag
+           {:flag "--concurrency" :key :concurrency :parse :range-int :min 1 :max 20
+            :desc "Parallel workers for import/enrich, 1-20 (default: 8)"
+            :error-invalid :invalid-concurrency :error-missing :missing-concurrency-value}]
    :initial {}
    :positionals {:required 1 :error :no-repo-path :keys [:repo-path]}})
 
@@ -223,7 +226,7 @@
                   :error-invalid :invalid-max-iterations
                   :error-missing :missing-max-iterations-value}
                  {:flag "--continue-from" :key :continue-from :parse :string
-                  :desc "Session ID from a budget-exhausted run — resumes the agent"}
+                  :desc "Session ID from a budget-exhausted run — resumes the agent (place before <repo-path>)"}
                  db-dir-flag]
                 verbose-flags))
    :initial {:subcommand "ask"}
@@ -325,7 +328,7 @@
    "introspect" {:spec introspect-command-spec
                  :summary "Autonomous self-improvement loop (optimize prompts via benchmark)"
                  :usage "introspect [options] <repo-path>"
-                 :epilog "Runs an autonomous loop: propose prompt change, evaluate via benchmark,\nkeep if improved, revert if not. Uses an LLM to propose improvements and\nthe agent benchmark to evaluate them.\n\nTargets (comma-separated): examples (default), system-prompt, rules, code, train.\nThe :code target requires passing lint and compilation. The :train target retrains\nthe on-device ML model. Example: --target examples,system-prompt\nUse --max-hours or --max-cost for overnight runs."}
+                 :epilog "Runs an autonomous loop: propose prompt change, evaluate via benchmark,\nkeep if improved, revert if not. Uses an LLM to propose improvements and\nthe agent benchmark to evaluate them.\n\nTargets (comma-separated): examples, system-prompt, rules, code, train\n(default: all — LLM chooses based on benchmark results).\nThe :code target requires passing lint and compilation. The :train target retrains\nthe on-device ML model. Example: --target examples,system-prompt\nUse --max-hours or --max-cost for overnight runs."}
    "reseed"    {:spec {:flags [db-dir-flag]
                        :initial {:subcommand "reseed"}
                        :positionals {:required 0 :error nil :keys []}}
@@ -511,6 +514,11 @@
                    (assoc result :layers (mapv keyword (str/split layers-str #",")))
                    result)]
       (cond
+        (and (= :no-repo-path (:error result))
+             (:resume result)
+             (str/starts-with? (str (:resume result)) "/"))
+        (assoc result :error :resume-consumed-repo-path)
+
         (:error result) result
         ;; --fast: deterministic only, full layer only (cheapest mode)
         (:fast result)  (-> result

src/noumenon/main.clj

@@ -201,7 +201,10 @@
             sync-opts (cond-> (build-sync-opts opts)
                         analyze (assoc :meta-db (d/db meta-conn)))
             result    (sync/update-repo! conn repo-path repo-uri sync-opts)]
-        (when-not analyze
+        (if analyze
+          (log! (str "Next: run '" cli/program-name " ask -q \"...\" " repo-path
+                     "' or '" cli/program-name " query <query-name> " repo-path
+                     "' to explore the updated graph."))
           (log! (str "Next: run '" cli/program-name " analyze " repo-path
                      "' to enrich with semantic metadata.")))
         {:exit 0 :result result}))))
@@ -397,6 +400,7 @@
           (do (print-error! (str "Database \"" db-name "\" not found.")) {:exit 1})
           (do (db/delete-db client db-name)
               (log! (str "Deleted database \"" db-name "\"."))
+              (log! "WARNING: All analysis data has been destroyed. Re-running analyze may be expensive.")
               (log! (str "Re-import: " cli/program-name " import <repo-path>"))
               {:exit 0})))
       (let [names (db/list-db-dirs db-dir)]
@@ -441,17 +445,24 @@
    :rubric-hash        "Rubric"
    :answer-prompt-hash "Answer prompt"})
 
+(def ^:private hash-fields
+  #{:question-set-hash :rubric-hash :answer-prompt-hash})
+
 (defn- format-compat-error
   "Format a checkpoint compatibility error message."
   [mismatches]
   (str "Incompatible checkpoint. The benchmark configuration has changed "
-       "since this checkpoint was created. Start a fresh run without --resume.\n"
+       "since this checkpoint was created.\n"
        "Mismatched fields:\n"
        (str/join "\n"
-                 (map #(str "  " (get compat-field-labels (:field %) (name (:field %)))
-                            ": checkpoint=" (:checkpoint %)
-                            " current=" (:current %))
-                      mismatches))))
+                 (map (fn [{:keys [field checkpoint current]}]
+                        (let [label (get compat-field-labels field (name field))]
+                          (if (hash-fields field)
+                            (str "  " label ": (changed)")
+                            (str "  " label ": checkpoint=" checkpoint
+                                 " current=" current))))
+                      mismatches))
+       "\nStart a fresh run: " cli/program-name " benchmark <repo-path>"))
 
 (defn- do-benchmark-resume
   "Handle --resume path for benchmark. Returns {:exit n}."
@@ -684,6 +695,7 @@
    :unknown-subcommand           #(str "Unknown subcommand: " (:subcommand %)
                                        ". Run '" cli/program-name " --help' for available subcommands.")
    :no-repo-path                 "Missing <repo-path> argument."
+   :resume-consumed-repo-path   "Missing <repo-path> argument. Did --resume consume your repo-path? Place --resume after <repo-path>."
    :query-missing-args           "Missing <query-name> and <repo-path> arguments."
    :missing-db-dir-value         "Missing value for --db-dir."
    :missing-delete-value          "Missing database name for --delete."
@@ -724,7 +736,7 @@
   #{:no-args :unknown-subcommand})
 
 (def ^:private errors-with-subcommand-usage
-  #{:no-repo-path :missing-db-dir-value :unknown-flag
+  #{:no-repo-path :resume-consumed-repo-path :missing-db-dir-value :unknown-flag
     :ask-missing-question :ask-missing-args :query-missing-args
     :missing-param-value :invalid-param-value
     :invalid-concurrency :missing-concurrency-value