diff --git a/src/apm_cli/compilation/claude_formatter.py b/src/apm_cli/compilation/claude_formatter.py
index f06e5ef3..fe78fdda 100644
--- a/src/apm_cli/compilation/claude_formatter.py
+++ b/src/apm_cli/compilation/claude_formatter.py
@@ -291,7 +291,10 @@ def _generate_claude_content(
                 sections.append(f"## Files matching `{pattern}`")
                 sections.append("")
                 
-                for instruction in pattern_instructions:
+                for instruction in sorted(
+                    pattern_instructions,
+                    key=lambda i: portable_relpath(i.file_path, self.base_dir),
+                ):
                     content = instruction.content.strip()
                     if content:
                         # Add source attribution comment
diff --git a/src/apm_cli/compilation/context_optimizer.py b/src/apm_cli/compilation/context_optimizer.py
index 4fc4181d..256ecb32 100644
--- a/src/apm_cli/compilation/context_optimizer.py
+++ b/src/apm_cli/compilation/context_optimizer.py
@@ -172,8 +172,9 @@ def _get_all_files(self) -> List[Path]:
             self._file_list_cache = []
             for root, dirs, files in os.walk(self.base_dir):
                 # Skip hidden and excluded directories for performance
-                dirs[:] = [d for d in dirs if not d.startswith('.') and d not in DEFAULT_EXCLUDED_DIRNAMES]
-                for file in files:
+                # Sort to guarantee deterministic traversal order across filesystems
+                dirs[:] = sorted(d for d in dirs if not d.startswith('.') and d not in DEFAULT_EXCLUDED_DIRNAMES)
+                for file in sorted(files):
                     if not file.startswith('.'):
                         self._file_list_cache.append(Path(root) / file)
         return self._file_list_cache
diff --git a/src/apm_cli/compilation/distributed_compiler.py b/src/apm_cli/compilation/distributed_compiler.py
index 48c3214b..c986b8bb 100644
--- a/src/apm_cli/compilation/distributed_compiler.py
+++ b/src/apm_cli/compilation/distributed_compiler.py
@@ -536,7 +536,10 @@ def _generate_agents_content(
             sections.append(f"## Files matching `{pattern}`")
             sections.append("")
             
-            for instruction in pattern_instructions:
+            for instruction in sorted(
+                pattern_instructions,
+                key=lambda i: portable_relpath(i.file_path, self.base_dir),
+            ):
                 content = instruction.content.strip()
                 if content:
                     # Add source attribution for individual instructions
diff --git a/src/apm_cli/compilation/template_builder.py b/src/apm_cli/compilation/template_builder.py
index e9b945d2..fd8799d1 100644
--- a/src/apm_cli/compilation/template_builder.py
+++ b/src/apm_cli/compilation/template_builder.py
@@ -34,12 +34,12 @@ def build_conditional_sections(instructions: List[Instruction]) -> str:
     
     sections = []
     
-    for pattern, pattern_instructions in pattern_groups.items():
+    for pattern, pattern_instructions in sorted(pattern_groups.items()):
         sections.append(f"## Files matching `{pattern}`")
         sections.append("")
-        
+
         # Combine content from all instructions for this pattern
-        for instruction in pattern_instructions:
+        for instruction in sorted(pattern_instructions, key=lambda i: portable_relpath(i.file_path, Path.cwd())):
             content = instruction.content.strip()
             if content:
                 # Add source file comment before the content