Apply suggestions from code review

Author: atorralba

java/ql/lib/change-notes/2023-03-31-new-models-tr2284.md

@@ -4,5 +4,4 @@ category: minorAnalysis
 * Added models for the following packages:
   * java.io
   * java.lang.module
-  * java.nio.file.spi
   * org.apache.commons.io

java/ql/lib/ext/java.io.model.yml

@@ -5,14 +5,13 @@ extensions:
     data:
       - ["java.io", "File", True, "createTempFile", "(String,String,File)", "", "Argument[2]", "create-file", "ai-generated"]
       - ["java.io", "File", True, "renameTo", "(File)", "", "Argument[0]", "create-file", "ai-generated"]
-      - ["java.io", "File", True, "renameTo", "(File)", "", "Argument[0]", "create-file", "ai-generated"] # This could, depending on the platform, also remove the file if one already exists with that path: https://docs.oracle.com/javase/7/docs/api/java/io/File.html#renameTo(java.io.File).
       - ["java.io", "FileInputStream", True, "FileInputStream", "(File)", "", "Argument[0]", "read-file", "ai-generated"]
       - ["java.io", "FileInputStream", True, "FileInputStream", "(String)", "", "Argument[0]", "read-file", "ai-generated"]
       - ["java.io", "FileOutputStream", False, "FileOutputStream", "", "", "Argument[0]", "create-file", "manual"]
       - ["java.io", "FileOutputStream", False, "write", "", "", "Argument[0]", "write-file", "manual"]
       - ["java.io", "FileReader", True, "FileReader", "(File)", "", "Argument[0]", "read-file", "ai-generated"]
       - ["java.io", "FileReader", True, "FileReader", "(String)", "", "Argument[0]", "read-file", "ai-generated"]
-      - ["java.io", "FileSystem", True, "createDirectory", "(File)", "", "Argument[0]", "create-file", "ai-generated"] # not sure, may be worth having an extra label for creating a dir..
+      - ["java.io", "FileSystem", True, "createDirectory", "(File)", "", "Argument[0]", "create-file", "ai-generated"]
       - ["java.io", "FileWriter", False, "FileWriter", "", "", "Argument[0]", "create-file", "manual"]
       - ["java.io", "PrintStream", False, "PrintStream", "(File)", "", "Argument[0]", "create-file", "manual"]
       - ["java.io", "PrintStream", False, "PrintStream", "(File,Charset)", "", "Argument[0]", "create-file", "manual"]

java/ql/lib/ext/java.lang.module.model.yml

@@ -1,6 +1,6 @@
 extensions:
   - addsTo:
       pack: codeql/java-all
-      extensible: sinkModel
+      extensible: summaryModel
     data:
-      - ["java.lang.module", "ModuleReader", True, "find", "(String)", "", "Argument[0]", "read-file", "ai-generated"] # The documentation implies that the location is actually read: https://docs.oracle.com/javase/9/docs/api/java/lang/module/ModuleReader.html#find-java.lang.String-
+      - ["java.lang.module", "ModuleReader", True, "find", "(String)", "", "Argument[0]", "ReturnValue", "taint", "ai-generated"]

java/ql/lib/ext/java.nio.file.spi.model.yml

@@ -16,6 +16,8 @@ extensions:
       pack: codeql/java-all
       extensible: sinkModel
     data:
-# suggested label is not supported:      - ["org.apache.commons.io", "FileUtils", True, "copyInputStreamToFile", "(InputStream,File)", "", "Argument[0]", "TODO", "ai-generated"]
-# suggested label is not supported:      - ["org.apache.commons.io", "FileUtils", True, "copyToFile", "(InputStream,File)", "", "Argument[0]", "TODO", "ai-generated"] # Not sure what this should be; the input stream is read from here - could be a file, could be memory, could be something else.
+      - ["org.apache.commons.io", "FileUtils", True, "copyInputStreamToFile", "(InputStream,File)", "", "Argument[0]", "write-file", "ai-generated"]
+      - ["org.apache.commons.io", "FileUtils", True, "copyInputStreamToFile", "(InputStream,File)", "", "Argument[1]", "create-file", "manual"]
+      - ["org.apache.commons.io", "FileUtils", True, "copyToFile", "(InputStream,File)", "", "Argument[0]", "write-file", "ai-generated"]
+      - ["org.apache.commons.io", "FileUtils", True, "copyToFile", "(InputStream,File)", "", "Argument[1]", "create-file", "manual"]
       - ["org.apache.commons.io", "FileUtils", True, "openInputStream", "(File)", "", "Argument[0]", "read-file", "ai-generated"]