Seperate code into sub branches under src/; add documentation.

Makefile

@@ -13,7 +13,24 @@ DEBUG_TARGET = opt6502-debug
 PROFILE_TARGET = opt6502-profile
 
 # Source files
-SOURCES = opt6502.c
+SOURCES = src/main.c \
+          src/types.c \
+          src/ast/ast.c \
+          src/ast/parser.c \
+          src/analysis/analysis.c \
+          src/analysis/registers.c \
+          src/optimizations/optimizer.c \
+          src/optimizations/peephole.c \
+          src/optimizations/deadcode.c \
+          src/optimizations/jumps.c \
+          src/optimizations/loadstore.c \
+          src/optimizations/regusage.c \
+          src/optimizations/constant.c \
+          src/optimizations/cpu65c02.c \
+          src/optimizations/cpu45gs02.c \
+          src/optimizations/inline.c \
+          src/output/output.c \
+          src/program/program.c
 OBJECTS = $(SOURCES:.c=.o)
 
 # Installation directory (can be overridden)
@@ -94,6 +111,7 @@ clean:
 	rm -f $(TARGET) $(DEBUG_TARGET) $(PROFILE_TARGET)
 	rm -f $(OBJECTS)
 	rm -f *.o
+	find src -name "*.o" -type f -delete 2>/dev/null || true
 	rm -f gmon.out
 	rm -f test_output.asm
 	@echo "Clean complete."
@@ -137,7 +155,7 @@ test: $(TARGET)
 dist: clean
 	@echo "Creating distribution tarball..."
 	@mkdir -p opt6502-1.0
-	@cp opt6502.c opt6502-1.0/
+	@cp -r src opt6502-1.0/
 	@cp Makefile opt6502-1.0/
 	@if [ -f README.md ]; then cp README.md opt6502-1.0/; fi
 	@if [ -f LICENSE ]; then cp LICENSE opt6502-1.0/; fi

src/analysis/analysis.c

@@ -0,0 +1,46 @@
+/**
+ * @file analysis.c
+ * @brief Code flow and branch target analysis implementation
+ *
+ * Implements control flow analysis functions for identifying branch
+ * targets and analyzing program structure.
+ */
+
+#include "analysis.h"
+
+/**
+ * @brief Mark all branch target labels in the AST
+ *
+ * Iterates through the AST and marks all label nodes as branch targets.
+ * Labels are potential targets for jumps, branches, and subroutine calls,
+ * so they must be preserved during optimization.
+ *
+ * @param prog Program to analyze
+ */
+void mark_branch_targets_ast(Program *prog) {
+    AstNode *node = prog->root;
+    while (node) {
+        if (node->type == NODE_LABEL) {
+            node->is_branch_target = true;
+        }
+        node = node->next;
+    }
+}
+
+/**
+ * @brief Analyze call flow and control flow patterns
+ *
+ * Wrapper function that performs all necessary control flow analysis.
+ * Currently calls mark_branch_targets_ast() to identify all labels
+ * that can be branched to.
+ *
+ * Future enhancements could include:
+ * - Dead code detection based on reachability
+ * - Loop detection
+ * - Subroutine call graph construction
+ *
+ * @param prog Program to analyze
+ */
+void analyze_call_flow_ast(Program *prog) {
+    mark_branch_targets_ast(prog);
+}

src/analysis/analysis.h

@@ -0,0 +1,36 @@
+/**
+ * @file analysis.h
+ * @brief Code flow and branch target analysis
+ *
+ * Provides analysis functions for identifying branch targets and
+ * analyzing control flow in the program AST.
+ */
+
+#ifndef ANALYSIS_H
+#define ANALYSIS_H
+
+#include "../types.h"
+
+/**
+ * @brief Mark all branch target labels in the AST
+ *
+ * Scans the AST and marks all label nodes that can be jumped or
+ * branched to. This information is used by optimizers to preserve
+ * labels that are referenced by control flow instructions.
+ *
+ * @param prog Program to analyze
+ */
+void mark_branch_targets_ast(Program *prog);
+
+/**
+ * @brief Analyze call flow and control flow patterns
+ *
+ * Performs control flow analysis including branch target identification.
+ * This is typically called before optimization passes to ensure that
+ * control flow is properly understood.
+ *
+ * @param prog Program to analyze
+ */
+void analyze_call_flow_ast(Program *prog);
+
+#endif // ANALYSIS_H