diff --git a/integration-test.sh b/integration-test.sh
index a6224ea..c58f1b0 100755
--- a/integration-test.sh
+++ b/integration-test.sh
@@ -11,35 +11,25 @@ SRCDIR=$HOME/Notes
 DSTDIR=$HOME/.second-brain
 EOF
 
-cat > $HOME/Notes/langchain.md <<EOF
-## References
-
-- https://docs.langchain.com/docs/
-- https://blog.langchain.dev/conversational-retrieval-agents/
-
-Plan-and-Solve Prompting: Improving Zero-Shot
-Chain-of-Thought Reasoning by Large Language Models
-https://arxiv.org/pdf/2305.04091.pdf
-EOF
-
 bash -x ./install-systemd-services.sh
 
 sleep 5
 
-TRY=0
+# wait for chromadb to be started
 docker-compose ps
 while [ $TRY -lt 24 ]; do
-    TRY=$(( TRY + 1 ))
+     TRY=$(( TRY + 1 ))
     if docker-compose logs | grep -q "Application startup complete"; then
+        echo "*** Found finished marker"
         break
-    fi
+     fi
     docker-compose logs
     sleep 5
 done
+docker-compose logs
+docker-compose logs | grep -q "Application startup complete"
 
-sudo journalctl -u sba-md
-sudo journalctl -u sba-txt
-
+# create the document
 cat > $HOME/Notes/langchain.md <<EOF
 ## References
 
@@ -51,6 +41,22 @@ Chain-of-Thought Reasoning by Large Language Models
 https://arxiv.org/pdf/2305.04091.pdf
 EOF
 
+# wait for the document to be processed
+TRY=0
+while [ $TRY -lt 30 ]; do
+    TRY=$(( TRY + 1 ))
+    if sudo journalctl -u sba-md | grep -q "processed '$HOME/Notes/langchain.md'"; then
+        echo "*** Found finished marker"
+        break
+    fi
+    sleep 1
+done
+
+sudo journalctl -u sba-md
+sudo journalctl -u sba-txt
+
+sudo journalctl -u sba-md | grep -q "processed '$HOME/Notes/langchain.md'"
+
 # test the vector store
 RES=$(poetry run ./similarity.py "What is langchain?")
 echo "$RES"
@@ -118,4 +124,38 @@ NB=$(sudo journalctl -u sba-md | grep -c "content is the same for")
 echo "*** NB=$NB"
 test "$NB" -eq 2
 
+# wait a bit to be sure to have all the logs in different seconds
+# for the vacuum cleaning process to work
+sleep 2
+
+# test removing a document
+sudo journalctl -u sba-md --rotate
+sudo journalctl -u sba-md --vacuum-time=1s
+sudo journalctl -u sba-txt --rotate
+sudo journalctl -u sba-txt --vacuum-time=1s
+
+rm "$HOME/Notes/langchain.md"
+
+TRY=0
+while [ $TRY -lt 5 ]; do
+    TRY=$(( TRY + 1 ))
+    if sudo journalctl -u sba-md | grep -q "removing $HOME/Text/langchain.json as $HOME/Notes/langchain.md do not exist anymore"; then
+        echo "*** Found finished marker"
+        break
+    fi
+    sleep 1
+done
+sudo journalctl -u sba-md | grep -q "removing $HOME/Text/langchain.json as $HOME/Notes/langchain.md do not exist anymore"
+
+TRY=0
+while [ $TRY -lt 5 ]; do
+    TRY=$(( TRY + 1 ))
+    if sudo journalctl -u sba-txt | grep -q "Removing $NB related files to $HOME/Text/langchain.json:"; then
+        echo "*** Found finished marker"
+        break
+    fi
+    sleep 1
+done
+sudo journalctl -u sba-txt | grep -q "Removing $NB related files to $HOME/Text/langchain.json:"
+
 # integration-test.sh ends here
diff --git a/monitor.sh b/monitor.sh
index cb4ae51..724e1cd 100755
--- a/monitor.sh
+++ b/monitor.sh
@@ -29,10 +29,8 @@ else
     . .venv/bin/activate
 fi
 
-
-
 "$TRANSFORM" "$SRC" "$DST"
 
-inotifywait -m -e CLOSE_WRITE "$SRC"|while read dir event fname; do echo "${dir}${fname} $event" 1>&2; echo "${dir}${fname}"; done | "$TRANSFORM" "-" "$DST"
+inotifywait -m -e CLOSE_WRITE,DELETE "$SRC"|while read dir event fname; do echo "${dir}${fname} $event" 1>&2; echo "${dir}${fname}"; done | "$TRANSFORM" "-" "$DST"
 
 # monitor.sh ends here
diff --git a/transform_md.py b/transform_md.py
index 1b7fb4a..4501396 100755
--- a/transform_md.py
+++ b/transform_md.py
@@ -8,6 +8,7 @@
 """
 
 import datetime
+import glob
 import hashlib
 import json
 import os
@@ -393,6 +394,22 @@ def process_md_file(fname, out_dir, checksum_store):
         return False
     basename = os.path.basename(fname[:-3])
     oname = get_output_file_path(out_dir, basename)
+    if not os.path.exists(fname):
+        print(f"removing {oname} as {fname} do not exist anymore", file=sys.stderr)
+        os.remove(oname)
+        if is_history_filename(fname):
+            for hname in glob.glob(
+                os.path.join(out_dir, "Markdown", basename + "*.md")
+            ):
+                basename = os.path.basename(hname[:-3])
+                oname = get_output_file_path(out_dir, basename)
+                print(
+                    f"removing {hname} / {oname} as {fname} do not exist anymore",
+                    file=sys.stderr,
+                )
+                os.remove(hname)
+                os.remove(oname)
+        return True
     if is_same_time(fname, oname):
         print(f"skipping {fname} as there is no time change", file=sys.stderr)
         return False
diff --git a/transform_txt.py b/transform_txt.py
index ba42e5f..ab1400b 100755
--- a/transform_txt.py
+++ b/transform_txt.py
@@ -73,10 +73,27 @@ def validate_and_extract_url(fname, basename, out_dir):
     return metadata, data["text"]
 
 
+def remove_related_files(fname, indexer, out_dir):
+    "Remove related files"
+    results = indexer.get(where={"main_source": {"$eq": fname}})
+    print(
+        f"Removing {len(results['ids'])} related files to {fname}: {' '.join(results['ids'])}",
+        file=sys.stderr,
+    )
+    if len(results["ids"]) > 0:
+        indexer.delete(results["ids"])
+        for chunk_id in results["ids"]:
+            os.remove(os.path.join(out_dir, "Chunk", chunk_id))
+
+
 def process_file(fname: str, out_dir: str, indexer, splitter):
     "Cut a text file in multiple chunks"
     basename = os.path.basename(fname[:-5])
     print(f"Processing '{fname}' '{basename}'", file=sys.stderr)
+    if not os.path.exists(fname):
+        print(f"File {fname} does not exist anymore", file=sys.stderr)
+        remove_related_files(fname, indexer, out_dir)
+        return
     metadata, content = validate_and_extract_url(fname, basename, out_dir)
     if metadata is False:
         return