diff --git a/.gitignore b/.gitignore
index a07072c..3260865 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+# Other files
+**/**/.venv
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -157,7 +160,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # vscode
 .vscode
@@ -165,11 +168,6 @@ cython_debug/
 # test data directory
 data
 
-# local manifests
-src/polus/plugins/_plugins/manifests/*
-
-# allow python scripts inside manifests dir
-!src/polus/plugins/_plugins/manifests/*.py
 
 #macOS
 *.DS_Store
diff --git a/clustering/feature-subsetting-tool/build-docker.sh b/clustering/feature-subsetting-tool/build-docker.sh
index 44cb5c2..ae5d5b6 100644
--- a/clustering/feature-subsetting-tool/build-docker.sh
+++ b/clustering/feature-subsetting-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/clustering/hdbscan-clustering-tool/build-docker.sh b/clustering/hdbscan-clustering-tool/build-docker.sh
index 349bd7e..3af8ada 100755
--- a/clustering/hdbscan-clustering-tool/build-docker.sh
+++ b/clustering/hdbscan-clustering-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/clustering/k-means-clustering-tool/build-docker.sh b/clustering/k-means-clustering-tool/build-docker.sh
index 3751895..a98c246 100644
--- a/clustering/k-means-clustering-tool/build-docker.sh
+++ b/clustering/k-means-clustering-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/clustering/outlier-removal-tool/build-docker.sh b/clustering/outlier-removal-tool/build-docker.sh
index 62e6aca..2cc5ea5 100644
--- a/clustering/outlier-removal-tool/build-docker.sh
+++ b/clustering/outlier-removal-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/features/feature-segmentation-eval-tool/build-docker.sh b/features/feature-segmentation-eval-tool/build-docker.sh
index 608a293..dba849b 100644
--- a/features/feature-segmentation-eval-tool/build-docker.sh
+++ b/features/feature-segmentation-eval-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/formats/tabular-converter-tool/build-docker.sh b/formats/tabular-converter-tool/build-docker.sh
index 976d0e1..1ec437f 100644
--- a/formats/tabular-converter-tool/build-docker.sh
+++ b/formats/tabular-converter-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/transforms/tabular-merger-tool/build-docker.sh b/transforms/tabular-merger-tool/build-docker.sh
index 8898286..9cd8135 100644
--- a/transforms/tabular-merger-tool/build-docker.sh
+++ b/transforms/tabular-merger-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/transforms/tabular-thresholding-tool/build-docker.sh b/transforms/tabular-thresholding-tool/build-docker.sh
index e91f426..088467f 100644
--- a/transforms/tabular-thresholding-tool/build-docker.sh
+++ b/transforms/tabular-thresholding-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/utils/rxiv-download-tool/build-docker.sh b/utils/rxiv-download-tool/build-docker.sh
index 0e3991d..bf99aae 100644
--- a/utils/rxiv-download-tool/build-docker.sh
+++ b/utils/rxiv-download-tool/build-docker.sh
@@ -16,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}