Determining the similarity between two documents
For flexibility, your cosineSimilarity() method should taken in List&lt;Integer&gt; arguments, instead of ArrayList&lt;Integer&gt; arguments.  This method doesn't care how the list is stored, only that it is a list which implements .size() and .get(i) methods.

For efficiency you should used double variables, not Double objects in the method:

public static double cosineSimilarity(List&lt;Integer&gt; vectorOne,
                                      List&lt;Integer&gt; vectorTwo)
    double dotProduct = 0.0;
    double normVecA = 0.0;
    double normVecB = 0.0;




When you open a Scanner, you should .close() it, to prevent resource leaks.  The "try-with-resources" construct will automatically close resources that it opens.  So instead of:

Scanner textFile = new Scanner(new File("Enter textfile  here"));


use

try(Scanner textFile = new Scanner(new File("Enter textfile  here")) {
    // use textFile inside this block.
}
// textFile is automatically closed when the block is exited.


Ditto with FileWriter.  Use "try-with-resources" to automatically close the writer.

try(FileWriter fw = new FileWriter(fileName, true)) {
    fw.write( ... );
}
// fw has been automatically closed at this point.




If you are using .nextInt(), you should loop on .hasNextInt(), not .hasNext().  

while(textFile.hasNextInt()) { 
     arsenal.add(textFile.nextInt());
} 




It sounds like you want a Map&lt;String,List&lt;Integer&gt;&gt; to store an ArrayList for each team.

List&lt;String&gt; team_names = List.of("Arsenal", "Chelsea", "Liverpool",
        "ManchesterCity", "ManchesterUnited", "Tottenham");

Map&lt;String,List&lt;Integer&gt;&gt; stats = new HashMap&lt;&gt;();

// Read in all team stats from (for example) "&lt;TeamName&gt;_stats.txt" files

for(String team_name : team_names) {
   List&lt;Integer&gt; team_stats = new ArrayList&lt;&gt;();
   try (Scanner textFile = new Scanner(new File(team+"_stats.txt"))) {
      while(textFile.hasNextInt()) {
          team_stats.add(textFile.nextInt());
      }
   }
   stats.put(team_name, team_stats);
}


Then you can use stats.get(team_name) to get each team's stats for comparison / analysis

for(String team1_name : team_names) {
   List&lt;Integer&gt; team1_stats = stats.get(team1_name);

   for(String team2_name: team_names) {
      // Skip comparing a team against itself
      if (team1_name.equals(team2_name))
          continue;

      List&lt;Integer&gt; team2_stats = stats.get(team2_name);

      double output = cosineSimilarity(team1_stats, team2_stats);

      // ... display "output", or write to file, or ...
   }
}


Depending on how you want your output written (one file for all comparisons, or one file per team for a comparison with all other teams, you'll want to open the FileWriter before the outer loop, or before the inner loop.