[compiler] misc scala 2.13 deprecation fixes (#15137)

## Change Description

The changes are summarized by the removed warning silencers in
`build.mill`​.

## Security Assessment

- This change cannot impact the Hail Batch instance as deployed by Broad
Institute in GCP

Author: patrick-schultz

hail/build.mill

@@ -147,27 +147,6 @@ trait HailModule extends ScalaModule with ScalafmtModule with ScalafixModule { o
     if (scalaVersion().startsWith("2.13")) {
       finalOptions ++
       Seq(
-      // collection types
-        // type Traversable in package scala is deprecated (since 2.13.0): Use Iterable instead of Traversable
-        "-Wconf:cat=deprecation&msg=type Traversable in package scala is deprecated:s",
-        // type TraversableOnce in package scala is deprecated (since 2.13.0): Use IterableOnce instead of TraversableOnce
-        "-Wconf:cat=deprecation&msg=type TraversableOnce:s",
-        // type BufferedIterator in package scala is deprecated (since 2.13.0): Use scala.collection.BufferedIterator instead of scala.BufferedIterator
-        "-Wconf:cat=deprecation&msg=type BufferedIterator in package scala is deprecated:s",
-        // class Stream in package immutable is deprecated (since 2.13.0): Use LazyList (which is fully lazy) instead of Stream (which has a lazy tail only)
-        "-Wconf:cat=deprecation&msg=Stream:s",
-        // type Growable in package generic is deprecated (since 2.13.0): Growable was moved from collection.generic to collection.mutable
-        "-Wconf:cat=deprecation&msg=type Growable in package generic is deprecated:s",
-        // type GenTraversableOnce in package collection is deprecated (since 2.13.0): Gen* collection types have been removed
-        "-Wconf:cat=deprecation&msg=type GenTraversableOnce in package collection is deprecated:s",
-        // trait MultiMap in package mutable is deprecated (since 2.13.0): Use a scala.collection.mutable.MultiDict in the scala-collection-contrib module
-        "-Wconf:cat=deprecation&msg=trait MultiMap in package mutable is deprecated:s",
-        // inheritance from class HashMap in package mutable is deprecated (since 2.13.0): HashMap will be made final; use .withDefault for the common use case of computing a default value
-        "-Wconf:cat=deprecation&msg=inheritance from class HashMap in package mutable is deprecated:s",
-        // object JavaConverters in package collection is deprecated (since 2.13.0): Use `scala.jdk.CollectionConverters` instead
-        "-Wconf:cat=deprecation&msg=object JavaConverters in package collection is deprecated:s",
-        // object ImplicitConversions in package convert is deprecated (since 2.13.0): Use `scala.jdk.CollectionConverters` instead
-        "-Wconf:cat=deprecation&msg=object ImplicitConversions in package convert is deprecated:s",
       // generic to immutable default
       // collection methods
         // method copyArrayToImmutableIndexedSeq in class LowPriorityImplicits2 is deprecated (since 2.13.0): implicit conversions from Array to immutable.IndexedSeq are implemented by copying; use `toIndexedSeq` explicitly if you want to copy, or use the more efficient non-copying ArraySeq.unsafeWrapArray
@@ -321,7 +300,6 @@ trait RootHailModule extends CrossScalaModule with HailModule { outer =>
     Rule.Exclude("META-INF/INDEX.LIST"),
     Rule.ExcludePattern("scala/(?!collection/compat).*"),
     Rule.AppendPattern("META-INF/services/.*", "\n"),
-//    Rule.Relocate("scala.collection.compat.**", "is.hail.relocated.@0"),
     Rule.Relocate("breeze.**", "is.hail.relocated.@0"),
     Rule.Relocate("com.google.cloud.**", "is.hail.relocated.@0"),
     Rule.Relocate("com.google.common.**", "is.hail.relocated.@0"),

hail/hail/src-2.12/is/hail/utils/compat/ShrinkableCompat.scala

@@ -1,8 +1,8 @@
-package is.hail.utils.compat
+package is.hail.utils.compat.mutable
 
-import scala.collection.generic.Growable
+import scala.collection.generic
 
-trait GrowableCompat[-A] extends Growable[A] {
+trait Growable[-A] extends generic.Growable[A] {
   override def +=(elem: A): this.type = addOne(elem)
   protected def addOne(elem: A): this.type
   def knownSize: Int = -1

…s/hail/utils/compat/GrowableCompat.scala …tils/compat/mutable/GrowableCompat.scalahail/hail/src-2.12/is/hail/utils/compat/GrowableCompat.scala renamed to hail/hail/src-2.12/is/hail/utils/compat/mutable/GrowableCompat.scala hail/hail/src-2.12/is/hail/utils/compat/GrowableCompat.scala renamed to hail/hail/src-2.12/is/hail/utils/compat/mutable/GrowableCompat.scala

@@ -0,0 +1,8 @@
+package is.hail.utils.compat.mutable
+
+import scala.collection.generic
+
+trait Shrinkable[-A] extends generic.Shrinkable[A] {
+  override def -=(elem: A): this.type = subtractOne(elem)
+  protected def subtractOne(elem: A): this.type
+}

hail/hail/src-2.12/is/hail/utils/compat/mutable/ShrinkableCompat.scala

@@ -2,7 +2,5 @@ package is.hail.utils.compat
 
 package object immutable {
   type ArraySeq[+A] = scala.collection.immutable.ArraySeq[A]
-
-  val ArraySeq: scala.collection.compat.immutable.ArraySeq.type =
-    scala.collection.compat.immutable.ArraySeq
+  val ArraySeq = scala.collection.immutable.ArraySeq
 }

hail/hail/src-2.13/is/hail/utils/compat/immutable/package.scala

@@ -0,0 +1,6 @@
+package is.hail.utils.compat
+
+package object mutable {
+  type Growable[-A] = scala.collection.mutable.Growable[A]
+  type Shrinkable[-A] = scala.collection.mutable.Shrinkable[A]
+}

hail/hail/src-2.13/is/hail/utils/compat/mutable/package.scala

@@ -4,8 +4,8 @@ import is.hail.backend.HailStateManager
 import is.hail.rvd.{RVDContext, RVDType}
 import is.hail.types.physical.PInterval
 import is.hail.utils._
+import is.hail.utils.compat.mutable.Growable
 
-import scala.collection.generic.Growable
 import scala.collection.mutable
 
 object OrderedRVIterator {

hail/hail/src-2.13/is/hail/utils/compat/package.scala

@@ -3,7 +3,7 @@ package is.hail.annotations
 import is.hail.backend.HailStateManager
 import is.hail.rvd.RVDContext
 import is.hail.types.physical.{PStruct, PType}
-import is.hail.utils.compat.GrowableCompat
+import is.hail.utils.compat.mutable.Growable
 
 import scala.collection.mutable.{ArrayBuffer, PriorityQueue}
 
@@ -129,7 +129,7 @@ class RegionValuePriorityQueue(
 }
 
 class RegionValueArrayBuffer(val t: PType, region: Region, sm: HailStateManager)
-    extends Iterable[RegionValue] with GrowableCompat[RegionValue] {
+    extends Iterable[RegionValue] with Growable[RegionValue] {
 
   val value = RegionValue(region, 0)
 

hail/hail/src/is/hail/annotations/OrderedRVIterator.scala

@@ -257,7 +257,7 @@ class ServiceBackend(
                   val (failures, successes) =
                     Await.result(
                       Future
-                        .traverse(failedJobs.map(_.take(1)) append succeededJobs) { jobs =>
+                        .traverse(failedJobs.map(_.take(1)) lazyAppendedAll succeededJobs) { jobs =>
                           readPartitionOutputs(jobs.map(_.job_id - startJobId))
                         },
                       Duration.Inf,