fix(cli): translate Commander --no-stats into noStats option (#704)

Commander's negatable-boolean convention sets options.stats = false when
--no-stats is passed, not options.noStats = true. The three call sites
that forward CLI options into runFullAnalysis / generateAIContextFiles
read options.noStats, so the flag was silently ignored and symbol counts
always got written into AGENTS.md / CLAUDE.md.

Fix: add ?? (options?.stats === false) fallback at all three call sites.

gitnexus/src/cli/analyze.ts

@@ -228,7 +228,7 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
         embeddings: options?.embeddings,
         skipGit: options?.skipGit,
         skipAgentsMd: options?.skipAgentsMd,
-        noStats: options?.noStats,
+        noStats: options?.noStats ?? (options?.stats === false),
         registryName: options?.name,
         // Registry-collision bypass — its own CLI flag, intentionally NOT
         // overloading --force. A user who hits the collision guard should
@@ -298,7 +298,7 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
               processes: s.processes,
             },
             skillResult.skills,
-            { skipAgentsMd: options?.skipAgentsMd, noStats: options?.noStats },
+            { skipAgentsMd: options?.skipAgentsMd, noStats: options?.noStats ?? (options?.stats === false) },
           );
         }
       } catch {

gitnexus/src/core/run-analyze.ts

@@ -379,7 +379,7 @@ export async function runFullAnalysis(
           processes: pipelineResult.processResult?.stats.totalProcesses,
         },
         undefined,
-        { skipAgentsMd: options.skipAgentsMd, noStats: options.noStats },
+        { skipAgentsMd: options.skipAgentsMd, noStats: options.noStats ?? (options.stats === false) },
       );
     } catch {
       // Best-effort — don't fail the entire analysis for context file issues