diff --git a/src/skill_seekers/cli/adaptors/claude.py b/src/skill_seekers/cli/adaptors/claude.py
index ea9f78c..1a275af 100644
--- a/src/skill_seekers/cli/adaptors/claude.py
+++ b/src/skill_seekers/cli/adaptors/claude.py
@@ -422,8 +422,8 @@ version: {metadata.version}
         references = {}
         total_chars = 0
 
-        # Read all .md files
-        for ref_file in sorted(references_dir.glob("*.md")):
+        # Read all .md files recursively (including subdirectories)
+        for ref_file in sorted(references_dir.rglob("*.md")):
             if total_chars >= max_chars:
                 break
 
diff --git a/src/skill_seekers/cli/adaptors/gemini.py b/src/skill_seekers/cli/adaptors/gemini.py
index b21a865..21ee238 100644
--- a/src/skill_seekers/cli/adaptors/gemini.py
+++ b/src/skill_seekers/cli/adaptors/gemini.py
@@ -237,7 +237,7 @@ See the references directory for complete documentation with examples and best p
                 refs_dir = temp_path / "references"
                 uploaded_refs = []
                 if refs_dir.exists():
-                    for ref_file in refs_dir.glob("*.md"):
+                    for ref_file in refs_dir.rglob("*.md"):
                         ref_uploaded = genai.upload_file(
                             path=str(ref_file), display_name=f"{package_path.stem}_{ref_file.stem}"
                         )
@@ -382,8 +382,8 @@ See the references directory for complete documentation with examples and best p
         references = {}
         total_chars = 0
 
-        # Read all .md files
-        for ref_file in sorted(references_dir.glob("*.md")):
+        # Read all .md files recursively (including subdirectories)
+        for ref_file in sorted(references_dir.rglob("*.md")):
             if total_chars >= max_chars:
                 break
 
diff --git a/src/skill_seekers/cli/adaptors/openai.py b/src/skill_seekers/cli/adaptors/openai.py
index 511ab02..e218d54 100644
--- a/src/skill_seekers/cli/adaptors/openai.py
+++ b/src/skill_seekers/cli/adaptors/openai.py
@@ -264,7 +264,7 @@ Always prioritize accuracy by consulting the attached documentation files before
                 file_ids = []
 
                 if vector_files_dir.exists():
-                    for ref_file in vector_files_dir.glob("*.md"):
+                    for ref_file in vector_files_dir.rglob("*.md"):
                         # Upload file
                         with open(ref_file, "rb") as f:
                             uploaded_file = client.files.create(file=f, purpose="assistants")
@@ -433,8 +433,8 @@ Always prioritize accuracy by consulting the attached documentation files before
         references = {}
         total_chars = 0
 
-        # Read all .md files
-        for ref_file in sorted(references_dir.glob("*.md")):
+        # Read all .md files recursively (including subdirectories)
+        for ref_file in sorted(references_dir.rglob("*.md")):
             if total_chars >= max_chars:
                 break