Python: Remove imprecise container steps

- remove `tupleStoreStep` and `dictStoreStep` from `containerStep`
   These are imprecise compared to the content being precise.
- add implicit reads to recover taint at sinks
- add implicit read steps for decoders
  to supplement the `AdditionalTaintStep`
  that now only covers when the full container is tainted.

python/ql/lib/semmle/python/dataflow/new/internal/DataFlowPrivate.qll

@@ -1009,6 +1009,8 @@ predicate readStep(Node nodeFrom, ContentSet c, Node nodeTo) {
   synthDictSplatParameterNodeReadStep(nodeFrom, c, nodeTo)
   or
   VariableCapture::readStep(nodeFrom, c, nodeTo)
+  or
+  Conversions::readStep(nodeFrom, c, nodeTo)
 }
 
 /** Data flows from a sequence to a subscript of the sequence. */
@@ -1064,6 +1066,40 @@ predicate attributeReadStep(Node nodeFrom, AttributeContent c, AttrRead nodeTo)
   nodeTo.accesses(nodeFrom, c.getAttribute())
 }
 
+module Conversions {
+  private import semmle.python.Concepts
+
+  predicate decoderReadStep(Node nodeFrom, ContentSet c, Node nodeTo) {
+    exists(Decoding decoding |
+      nodeFrom = decoding.getAnInput() and
+      nodeTo = decoding.getOutput()
+    ) and
+    (
+      c instanceof TupleElementContent
+      or
+      c instanceof DictionaryElementContent
+    )
+  }
+
+  predicate encoderReadStep(Node nodeFrom, ContentSet c, Node nodeTo) {
+    exists(Encoding encoding |
+      nodeFrom = encoding.getAnInput() and
+      nodeTo = encoding.getOutput()
+    ) and
+    (
+      c instanceof TupleElementContent
+      or
+      c instanceof DictionaryElementContent
+    )
+  }
+
+  predicate readStep(Node nodeFrom, ContentSet c, Node nodeTo) {
+    decoderReadStep(nodeFrom, c, nodeTo)
+    or
+    encoderReadStep(nodeFrom, c, nodeTo)
+  }
+}
+
 /**
  * Holds if values stored inside content `c` are cleared at node `n`. For example,
  * any value stored inside `f` is cleared at the pre-update node associated with `x`

python/ql/lib/semmle/python/dataflow/new/internal/TaintTrackingPrivate.qll

@@ -16,7 +16,16 @@ predicate defaultTaintSanitizer(DataFlow::Node node) { none() }
  * of `c` at sinks and inputs to additional taint steps.
  */
 bindingset[node]
-predicate defaultImplicitTaintRead(DataFlow::Node node, DataFlow::ContentSet c) { none() }
+predicate defaultImplicitTaintRead(DataFlow::Node node, DataFlow::ContentSet c) {
+  // We allow implicit reads of precise content
+  // imprecise content has already bubled up.
+  exists(node) and
+  (
+    c instanceof DataFlow::TupleElementContent
+    or
+    c instanceof DataFlow::DictionaryElementContent
+  )
+}
 
 private module Cached {
   /**
@@ -176,10 +185,6 @@ predicate containerStep(DataFlow::Node nodeFrom, DataFlow::Node nodeTo) {
   or
   DataFlowPrivate::setStoreStep(nodeFrom, _, nodeTo)
   or
-  DataFlowPrivate::tupleStoreStep(nodeFrom, _, nodeTo)
-  or
-  DataFlowPrivate::dictStoreStep(nodeFrom, _, nodeTo)
-  or
   // comprehension, so there is taint-flow from `x` in `[x for x in xs]` to the
   // resulting list of the list-comprehension.
   //