diff --git a/lib/src/index.rs b/lib/src/index.rs
index 696e9b5c1..5bb7ed9b6 100644
--- a/lib/src/index.rs
+++ b/lib/src/index.rs
@@ -138,39 +138,43 @@ struct CommitGraphEntry<'a> {
 // lowest set bit to determine which generation number the pointers point to.
 impl CommitGraphEntry<'_> {
     fn size(hash_length: usize) -> usize {
-        28 + hash_length
+        32 + hash_length
+    }
+
+    fn is_pruned(&self) -> bool {
+        (&self.data[0..]).read_u32::<LittleEndian>().unwrap() != 0
     }
 
     fn generation_number(&self) -> u32 {
-        (&self.data[0..]).read_u32::<LittleEndian>().unwrap()
-    }
-
-    fn num_parents(&self) -> u32 {
         (&self.data[4..]).read_u32::<LittleEndian>().unwrap()
     }
 
-    fn parent1_pos(&self) -> u32 {
+    fn num_parents(&self) -> u32 {
         (&self.data[8..]).read_u32::<LittleEndian>().unwrap()
     }
 
-    fn parent2_overflow_pos(&self) -> u32 {
+    fn parent1_pos(&self) -> u32 {
         (&self.data[12..]).read_u32::<LittleEndian>().unwrap()
     }
 
-    fn num_predecessors(&self) -> u32 {
+    fn parent2_overflow_pos(&self) -> u32 {
         (&self.data[16..]).read_u32::<LittleEndian>().unwrap()
     }
 
-    fn predecessor1_pos(&self) -> u32 {
+    fn num_predecessors(&self) -> u32 {
         (&self.data[20..]).read_u32::<LittleEndian>().unwrap()
     }
 
-    fn predecessor2_overflow_pos(&self) -> u32 {
+    fn predecessor1_pos(&self) -> u32 {
         (&self.data[24..]).read_u32::<LittleEndian>().unwrap()
     }
 
+    fn predecessor2_overflow_pos(&self) -> u32 {
+        (&self.data[28..]).read_u32::<LittleEndian>().unwrap()
+    }
+
     fn commit_id(&self) -> CommitId {
-        CommitId(self.data[28..28 + self.hash_length].to_vec())
+        CommitId(self.data[32..32 + self.hash_length].to_vec())
     }
 }
 
@@ -360,6 +364,7 @@ impl PrefixResolution {
 #[derive(Debug)]
 struct MutableGraphEntry {
     commit_id: CommitId,
+    is_pruned: bool,
     generation_number: u32,
     parent_positions: Vec<u32>,
     predecessor_positions: Vec<u32>,
@@ -406,6 +411,7 @@ impl MutableIndex {
     pub fn add_commit(&mut self, commit: &Commit) {
         self.add_commit_data(
             commit.id().clone(),
+            commit.is_pruned(),
             commit.parent_ids(),
             commit.predecessor_ids(),
         );
@@ -414,6 +420,7 @@ impl MutableIndex {
     fn add_commit_data(
         &mut self,
         id: CommitId,
+        is_pruned: bool,
         parent_ids: Vec<CommitId>,
         predecessor_ids: Vec<CommitId>,
     ) {
@@ -422,6 +429,7 @@ impl MutableIndex {
         }
         let mut entry = MutableGraphEntry {
             commit_id: id,
+            is_pruned,
             generation_number: 0,
             parent_positions: vec![],
             predecessor_positions: vec![],
@@ -475,6 +483,9 @@ impl MutableIndex {
         let mut parent_overflow = vec![];
         let mut predecessor_overflow = vec![];
         for entry in self.graph {
+            let flags = if entry.is_pruned { 1 } else { 0 };
+            buf.write_u32::<LittleEndian>(flags).unwrap();
+
             buf.write_u32::<LittleEndian>(entry.generation_number)
                 .unwrap();
 
@@ -574,7 +585,12 @@ impl MutableIndex {
                 .iter()
                 .map(|pos| self.entry_by_pos(*pos).commit_id())
                 .collect();
-            squashed.add_commit_data(entry.commit_id(), parent_ids, predecessor_ids);
+            squashed.add_commit_data(
+                entry.commit_id(),
+                entry.is_pruned(),
+                parent_ids,
+                predecessor_ids,
+            );
         }
         squashed
     }
@@ -663,6 +679,8 @@ trait IndexSegment {
 
     fn segment_resolve_prefix(&self, prefix: &HexPrefix) -> PrefixResolution;
 
+    fn segment_is_pruned(&self, local_pos: u32) -> bool;
+
     fn segment_generation_number(&self, local_pos: u32) -> u32;
 
     fn segment_commit_id(&self, local_pos: u32) -> CommitId;
@@ -1089,6 +1107,11 @@ impl IndexSegment for ReadonlyIndex {
         }
     }
 
+    fn segment_is_pruned(&self, local_pos: u32) -> bool {
+        let graph_entry = self.graph_entry(local_pos);
+        graph_entry.is_pruned()
+    }
+
     fn segment_generation_number(&self, local_pos: u32) -> u32 {
         self.graph_entry(local_pos).generation_number()
     }
@@ -1197,6 +1220,10 @@ impl IndexSegment for MutableIndex {
         }
     }
 
+    fn segment_is_pruned(&self, local_pos: u32) -> bool {
+        self.graph[local_pos as usize].is_pruned
+    }
+
     fn segment_generation_number(&self, local_pos: u32) -> u32 {
         self.graph[local_pos as usize].generation_number
     }
@@ -1254,6 +1281,10 @@ impl IndexEntry<'_> {
         self.source.segment_commit_id(self.local_pos)
     }
 
+    fn is_pruned(&self) -> bool {
+        self.source.segment_is_pruned(self.local_pos)
+    }
+
     pub fn num_parents(&self) -> u32 {
         self.source.segment_num_parents(self.local_pos)
     }
@@ -1574,7 +1605,7 @@ mod tests {
         let temp_dir = tempfile::tempdir().unwrap();
         let mut index = MutableIndex::full(temp_dir.path().to_owned(), 3);
         let id_0 = CommitId::from_hex("000000");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
         let index = if on_disk {
             IndexRef::Readonly(index.save().unwrap())
         } else {
@@ -1610,7 +1641,7 @@ mod tests {
         let mut index = MutableIndex::full(temp_dir.path().to_owned(), 3);
         let id_0 = CommitId::from_hex("000000");
         let id_1 = CommitId::from_hex("111111");
-        index.add_commit_data(id_1, vec![id_0], vec![]);
+        index.add_commit_data(id_1, false, vec![id_0], vec![]);
     }
 
     #[test_case(false, false; "full in memory")]
@@ -1630,9 +1661,9 @@ mod tests {
         let id_0 = CommitId::from_hex("000000");
         let id_1 = CommitId::from_hex("111111");
         let id_2 = CommitId::from_hex("222222");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
 
         // If testing incremental indexing, write the first three commits to one file
         // now and build the remainder as another segment on top.
@@ -1644,13 +1675,19 @@ mod tests {
         let id_3 = CommitId::from_hex("333333");
         let id_4 = CommitId::from_hex("444444");
         let id_5 = CommitId::from_hex("555555");
-        index.add_commit_data(id_3.clone(), vec![id_2.clone()], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![id_2.clone()], vec![]);
         index.add_commit_data(
             id_4.clone(),
+            false,
             vec![id_1.clone()],
             vec![id_2.clone(), id_3.clone()],
         );
-        index.add_commit_data(id_5.clone(), vec![id_4.clone(), id_2.clone()], vec![]);
+        index.add_commit_data(
+            id_5.clone(),
+            false,
+            vec![id_4.clone(), id_2.clone()],
+            vec![],
+        );
         let index = if on_disk {
             IndexRef::Readonly(index.save().unwrap())
         } else {
@@ -1722,14 +1759,15 @@ mod tests {
         let id_4 = CommitId::from_hex("444444");
         let id_5 = CommitId::from_hex("555555");
         let id_6 = CommitId::from_hex("666666");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_3.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_4.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_5.clone(), vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_4.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_5.clone(), false, vec![id_0.clone()], vec![]);
         index.add_commit_data(
             id_6.clone(),
+            false,
             vec![
                 id_1.clone(),
                 id_2.clone(),
@@ -1769,9 +1807,9 @@ mod tests {
         let id_0 = CommitId::from_hex("000000");
         let id_1 = CommitId::from_hex("009999");
         let id_2 = CommitId::from_hex("055488");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![], vec![]);
-        index.add_commit_data(id_2.clone(), vec![], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![], vec![]);
 
         // Write the first three commits to one file and build the remainder on top.
         let initial_file = index.save().unwrap();
@@ -1780,9 +1818,9 @@ mod tests {
         let id_3 = CommitId::from_hex("055444");
         let id_4 = CommitId::from_hex("055555");
         let id_5 = CommitId::from_hex("033333");
-        index.add_commit_data(id_3.clone(), vec![], vec![]);
-        index.add_commit_data(id_4.clone(), vec![], vec![]);
-        index.add_commit_data(id_5.clone(), vec![], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_4.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_5.clone(), false, vec![], vec![]);
 
         // Can find commits given the full hex number
         assert_eq!(
@@ -1844,12 +1882,17 @@ mod tests {
         let id_3 = CommitId::from_hex("333333");
         let id_4 = CommitId::from_hex("444444");
         let id_5 = CommitId::from_hex("555555");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_3.clone(), vec![id_2.clone()], vec![]);
-        index.add_commit_data(id_4.clone(), vec![id_1.clone()], vec![]);
-        index.add_commit_data(id_5.clone(), vec![id_4.clone(), id_2.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![id_2.clone()], vec![]);
+        index.add_commit_data(id_4.clone(), false, vec![id_1.clone()], vec![]);
+        index.add_commit_data(
+            id_5.clone(),
+            false,
+            vec![id_4.clone(), id_2.clone()],
+            vec![],
+        );
 
         assert!(index.is_ancestor(&id_0, &id_0));
         assert!(index.is_ancestor(&id_0, &id_1));
@@ -1882,12 +1925,17 @@ mod tests {
         let id_3 = CommitId::from_hex("333333");
         let id_4 = CommitId::from_hex("444444");
         let id_5 = CommitId::from_hex("555555");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_3.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_4.clone(), vec![id_1.clone()], vec![]);
-        index.add_commit_data(id_5.clone(), vec![id_4.clone(), id_2.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_4.clone(), false, vec![id_1.clone()], vec![]);
+        index.add_commit_data(
+            id_5.clone(),
+            false,
+            vec![id_4.clone(), id_2.clone()],
+            vec![],
+        );
 
         assert_eq!(
             index.common_ancestors(&[id_0.clone()], &[id_0.clone()]),
@@ -1963,11 +2011,21 @@ mod tests {
         let id_2 = CommitId::from_hex("222222");
         let id_3 = CommitId::from_hex("333333");
         let id_4 = CommitId::from_hex("444444");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_3.clone(), vec![id_1.clone(), id_2.clone()], vec![]);
-        index.add_commit_data(id_4.clone(), vec![id_1.clone(), id_2.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(
+            id_3.clone(),
+            false,
+            vec![id_1.clone(), id_2.clone()],
+            vec![],
+        );
+        index.add_commit_data(
+            id_4.clone(),
+            false,
+            vec![id_1.clone(), id_2.clone()],
+            vec![],
+        );
 
         let mut common_ancestors = index.common_ancestors(&[id_3.clone()], &[id_4.clone()]);
         common_ancestors.sort();
@@ -1989,12 +2047,22 @@ mod tests {
         let id_3 = CommitId::from_hex("333333");
         let id_4 = CommitId::from_hex("444444");
         let id_5 = CommitId::from_hex("555555");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_3.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_4.clone(), vec![id_0.clone(), id_2.clone()], vec![]);
-        index.add_commit_data(id_5.clone(), vec![id_0.clone(), id_2.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(
+            id_4.clone(),
+            false,
+            vec![id_0.clone(), id_2.clone()],
+            vec![],
+        );
+        index.add_commit_data(
+            id_5.clone(),
+            false,
+            vec![id_0.clone(), id_2.clone()],
+            vec![],
+        );
 
         let mut common_ancestors = index.common_ancestors(&[id_4.clone()], &[id_5.clone()]);
         common_ancestors.sort();
@@ -2018,12 +2086,17 @@ mod tests {
         let id_3 = CommitId::from_hex("333333");
         let id_4 = CommitId::from_hex("444444");
         let id_5 = CommitId::from_hex("555555");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_3.clone(), vec![id_2.clone()], vec![]);
-        index.add_commit_data(id_4.clone(), vec![id_1.clone()], vec![]);
-        index.add_commit_data(id_5.clone(), vec![id_4.clone(), id_2.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![id_2.clone()], vec![]);
+        index.add_commit_data(id_4.clone(), false, vec![id_1.clone()], vec![]);
+        index.add_commit_data(
+            id_5.clone(),
+            false,
+            vec![id_4.clone(), id_2.clone()],
+            vec![],
+        );
 
         // No wanted commits
         let revs: Vec<CommitId> = index.walk_revs(&[], &[]).collect();
@@ -2086,12 +2159,17 @@ mod tests {
         let id_3 = CommitId::from_hex("333333");
         let id_4 = CommitId::from_hex("444444");
         let id_5 = CommitId::from_hex("555555");
-        index.add_commit_data(id_0.clone(), vec![], vec![]);
-        index.add_commit_data(id_1.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_2.clone(), vec![id_0.clone()], vec![]);
-        index.add_commit_data(id_3.clone(), vec![id_2.clone()], vec![]);
-        index.add_commit_data(id_4.clone(), vec![id_1.clone()], vec![]);
-        index.add_commit_data(id_5.clone(), vec![id_4.clone(), id_2.clone()], vec![]);
+        index.add_commit_data(id_0.clone(), false, vec![], vec![]);
+        index.add_commit_data(id_1.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_2.clone(), false, vec![id_0.clone()], vec![]);
+        index.add_commit_data(id_3.clone(), false, vec![id_2.clone()], vec![]);
+        index.add_commit_data(id_4.clone(), false, vec![id_1.clone()], vec![]);
+        index.add_commit_data(
+            id_5.clone(),
+            false,
+            vec![id_4.clone(), id_2.clone()],
+            vec![],
+        );
 
         // Empty input
         assert!(index.heads(&[]).is_empty());