Patch potentually fit peaks getting out of sync/re-ordered when concatanated batch peak fit file has cleanup_after_load.

I didnt see this happening on example scenerious I ran, probably because all sample numbers are unique, so it shouldnt happen - but made these changes JIC.

Author: wcjohns

src/BatchPeak.cpp

@@ -710,10 +710,13 @@ void fit_peaks_in_files( const std::string &exemplar_filename,
           concatenated_spec->setPeaks( peaks_copy, sample_nums );
         }
       }
-      
+
+      // TODO: Sort sample numbers according to start time, and call:
+      //concatenated_spec->change_sample_numbers(<#const std::vector<std::pair<int, int>> &from_to_sample_nums#>);
+
       // Clean up the SpecMeas after adding all measurements
-      concatenated_spec->cleanup_after_load();
-      
+      concatenated_spec->cleanup_after_load( SpecUtils::SpecFile::DontChangeOrReorderSamples );
+
       // Save the concatenated file
       const string concatenated_file = SpecUtils::append_path( options.output_dir, "concatenated.n42" );
 

src/SpecMeas.cpp

@@ -2586,7 +2586,18 @@ const map<set<int>,long long int> &SpecMeas::dbUserStateIndexes() const
 
 void SpecMeas::cleanup_after_load( const unsigned int flags )
 {
-  if( m_fileWasFromInterSpec )
+  bool has_any_peaks = false;
+  if( m_peaks )
+  {
+    for( const auto &samples_peaks : *m_peaks )
+    {
+      has_any_peaks = (samples_peaks.second && !samples_peaks.second->empty());
+      if( has_any_peaks )
+        break;
+    }
+  }//if( m_peaks )
+
+  if( m_fileWasFromInterSpec || has_any_peaks )
   {
     SpecFile::cleanup_after_load( (flags | SpecFile::DontChangeOrReorderSamples) );
   }else