diff --git a/.gitignore b/.gitignore
index 7d2d0ed..faf2e5c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,11 +5,13 @@
 status.json
 
 # Logs
-logs/
+logs/*
+!logs/.gitkeep
 *.log
 
 # Generated documentation
-docs/generated/
+docs/generated/*
+!docs/generated/.gitkeep
 
 # OS files
 .DS_Store
diff --git a/docs/generated/.gitkeep b/docs/generated/.gitkeep
new file mode 100644
index 0000000..0406914
--- /dev/null
+++ b/docs/generated/.gitkeep
@@ -0,0 +1,3 @@
+# This file ensures the docs/generated/ directory is tracked by git
+# Note: Generated documentation files are ignored by .gitignore
+# This directory is needed for Ralph loop execution
\ No newline at end of file
diff --git a/examples/.gitkeep b/examples/.gitkeep
new file mode 100644
index 0000000..ddb08c6
--- /dev/null
+++ b/examples/.gitkeep
@@ -0,0 +1,2 @@
+# This file ensures the examples/ directory is tracked by git
+# Remove this file when you add actual example files
\ No newline at end of file
diff --git a/logs/.gitkeep b/logs/.gitkeep
new file mode 100644
index 0000000..544fad2
--- /dev/null
+++ b/logs/.gitkeep
@@ -0,0 +1,3 @@
+# This file ensures the logs/ directory is tracked by git
+# Note: Actual log files are ignored by .gitignore
+# This directory is needed for Ralph loop execution
\ No newline at end of file
diff --git a/specs/stdlib/.gitkeep b/specs/stdlib/.gitkeep
new file mode 100644
index 0000000..5f3b7da
--- /dev/null
+++ b/specs/stdlib/.gitkeep
@@ -0,0 +1,2 @@
+# This file ensures the specs/stdlib/ directory is tracked by git
+# Remove this file when you add actual specification files
\ No newline at end of file
diff --git a/src/.gitkeep b/src/.gitkeep
new file mode 100644
index 0000000..cc237b5
--- /dev/null
+++ b/src/.gitkeep
@@ -0,0 +1,2 @@
+# This file ensures the src/ directory is tracked by git
+# Remove this file when you add actual source files
\ No newline at end of file
diff --git a/templates/specs/.gitkeep b/templates/specs/.gitkeep
new file mode 100644
index 0000000..3e44682
--- /dev/null
+++ b/templates/specs/.gitkeep
@@ -0,0 +1,2 @@
+# This file ensures the templates/specs/ directory is tracked by git
+# Remove this file when you add actual template specification files
\ No newline at end of file