diff --git a/trustgraph-flow/pyproject.toml b/trustgraph-flow/pyproject.toml
index 9e041ccb..1a126959 100644
--- a/trustgraph-flow/pyproject.toml
+++ b/trustgraph-flow/pyproject.toml
@@ -56,44 +56,45 @@ Homepage = "https://github.com/trustgraph-ai/trustgraph"
 
 [project.scripts]
 agent-manager-react = "trustgraph.agent.react:run"
-api-gateway = "trustgraph.gateway.api:run"
-rev-gateway = "trustgraph.gateway.reverse:run"
-chunker-recursive = "trustgraph.chunker.recursive:run"
-chunker-token = "trustgraph.chunker.token:run"
+api-gateway = "trustgraph.gateway:run"
+chunker-recursive = "trustgraph.chunking.recursive:run"
+chunker-token = "trustgraph.chunking.token:run"
 config-svc = "trustgraph.config.service:run"
-de-query-milvus = "trustgraph.document_embeddings.query.milvus:run"
-de-query-pinecone = "trustgraph.document_embeddings.query.pinecone:run"
-de-query-qdrant = "trustgraph.document_embeddings.query.qdrant:run"
-de-write-milvus = "trustgraph.document_embeddings.write.milvus:run"
-de-write-pinecone = "trustgraph.document_embeddings.write.pinecone:run"
-de-write-qdrant = "trustgraph.document_embeddings.write.qdrant:run"
-document-embeddings = "trustgraph.model.embedding.document:run"
+de-query-milvus = "trustgraph.query.doc_embeddings.milvus:run"
+de-query-pinecone = "trustgraph.query.doc_embeddings.pinecone:run"
+de-query-qdrant = "trustgraph.query.doc_embeddings.qdrant:run"
+de-write-milvus = "trustgraph.storage.doc_embeddings.milvus:run"
+de-write-pinecone = "trustgraph.storage.doc_embeddings.pinecone:run"
+de-write-qdrant = "trustgraph.storage.doc_embeddings.qdrant:run"
+document-embeddings = "trustgraph.embeddings.document_embeddings:run"
 document-rag = "trustgraph.retrieval.document_rag:run"
 embeddings-fastembed = "trustgraph.embeddings.fastembed:run"
 embeddings-ollama = "trustgraph.embeddings.ollama:run"
-ge-query-milvus = "trustgraph.graph_embeddings.query.milvus:run"
-ge-query-pinecone = "trustgraph.graph_embeddings.query.pinecone:run"
-ge-query-qdrant = "trustgraph.graph_embeddings.query.qdrant:run"
-ge-write-milvus = "trustgraph.graph_embeddings.write.milvus:run"
-ge-write-pinecone = "trustgraph.graph_embeddings.write.pinecone:run"
-ge-write-qdrant = "trustgraph.graph_embeddings.write.qdrant:run"
-graph-embeddings = "trustgraph.model.embedding.graph:run"
+ge-query-milvus = "trustgraph.query.graph_embeddings.milvus:run"
+ge-query-pinecone = "trustgraph.query.graph_embeddings.pinecone:run"
+ge-query-qdrant = "trustgraph.query.graph_embeddings.qdrant:run"
+ge-write-milvus = "trustgraph.storage.graph_embeddings.milvus:run"
+ge-write-pinecone = "trustgraph.storage.graph_embeddings.pinecone:run"
+ge-write-qdrant = "trustgraph.storage.graph_embeddings.qdrant:run"
+graph-embeddings = "trustgraph.embeddings.graph_embeddings:run"
 graph-rag = "trustgraph.retrieval.graph_rag:run"
-kg-extract-definitions = "trustgraph.extract.definitions:run"
-kg-extract-relationships = "trustgraph.extract.relationships:run"
-kg-extract-agent = "trustgraph.extract.agent:run"
-kg-store = "trustgraph.cores.triples_store:run"
-kg-manager = "trustgraph.cores.manager:run"
-librarian = "trustgraph.processing.librarian:run"
-mcp-tool = "trustgraph.tool.mcp:run"
-metering = "trustgraph.metering.service:run"
-object-extract-row = "trustgraph.object.extract_row:run"
-oe-write-milvus = "trustgraph.object_embeddings.write.milvus:run"
-pdf-decoder = "trustgraph.decoding.pdf_decoder:run"
-pdf-ocr-mistral = "trustgraph.decoding.pdf_ocr_mistral:run"
+kg-extract-agent = "trustgraph.extract.kg.agent:run"
+kg-extract-definitions = "trustgraph.extract.kg.definitions:run"
+kg-extract-relationships = "trustgraph.extract.kg.relationships:run"
+kg-extract-topics = "trustgraph.extract.kg.topics:run"
+kg-manager = "trustgraph.cores:run"
+kg-store = "trustgraph.storage.knowledge:run"
+librarian = "trustgraph.librarian:run"
+mcp-tool = "trustgraph.agent.mcp_tool:run"
+metering = "trustgraph.metering:run"
+object-extract-row = "trustgraph.extract.object.row:run"
+oe-write-milvus = "trustgraph.storage.object_embeddings.milvus:run"
+pdf-decoder = "trustgraph.decoding.pdf:run"
+pdf-ocr-mistral = "trustgraph.decoding.mistral_ocr:run"
 prompt-template = "trustgraph.prompt.template:run"
-rows-write-cassandra = "trustgraph.rows.write.cassandra:run"
-run-processing = "trustgraph.processing.run:run"
+rev-gateway = "trustgraph.rev_gateway:run"
+rows-write-cassandra = "trustgraph.storage.rows.cassandra:run"
+run-processing = "trustgraph.processing:run"
 text-completion-azure = "trustgraph.model.text_completion.azure:run"
 text-completion-azure-openai = "trustgraph.model.text_completion.azure_openai:run"
 text-completion-claude = "trustgraph.model.text_completion.claude:run"
@@ -106,15 +107,15 @@ text-completion-ollama = "trustgraph.model.text_completion.ollama:run"
 text-completion-openai = "trustgraph.model.text_completion.openai:run"
 text-completion-tgi = "trustgraph.model.text_completion.tgi:run"
 text-completion-vllm = "trustgraph.model.text_completion.vllm:run"
-triples-query-cassandra = "trustgraph.triples.query.cassandra:run"
-triples-query-falkordb = "trustgraph.triples.query.falkordb:run"
-triples-query-memgraph = "trustgraph.triples.query.memgraph:run"
-triples-query-neo4j = "trustgraph.triples.query.neo4j:run"
-triples-write-cassandra = "trustgraph.triples.write.cassandra:run"
-triples-write-falkordb = "trustgraph.triples.write.falkordb:run"
-triples-write-memgraph = "trustgraph.triples.write.memgraph:run"
-triples-write-neo4j = "trustgraph.triples.write.neo4j:run"
-wikipedia-lookup = "trustgraph.retrieval.wikipedia_lookup:run"
+triples-query-cassandra = "trustgraph.query.triples.cassandra:run"
+triples-query-falkordb = "trustgraph.query.triples.falkordb:run"
+triples-query-memgraph = "trustgraph.query.triples.memgraph:run"
+triples-query-neo4j = "trustgraph.query.triples.neo4j:run"
+triples-write-cassandra = "trustgraph.storage.triples.cassandra:run"
+triples-write-falkordb = "trustgraph.storage.triples.falkordb:run"
+triples-write-memgraph = "trustgraph.storage.triples.memgraph:run"
+triples-write-neo4j = "trustgraph.storage.triples.neo4j:run"
+wikipedia-lookup = "trustgraph.external.wikipedia:run"
 
 [tool.setuptools]
 packages = ["trustgraph"]