diff --git a/Makefile.in b/Makefile.in
index 83757aa8c4..725e456720 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1092,9 +1092,11 @@ dist_man_MANS = Doxygen/man/man1/arangoimp.1 \
 ### @brief cleanup
 ################################################################################
 CLEANUP = .setup-js-directories .setup-mr-directories \
-	bin/arango-password bin/arango-upgrade bin/arango-dfdb \
-	$(DOXYGEN) $(addsuffix .md,$(addprefix Doxygen/xml/,$(WIKI))) \
-	$(addsuffix .md,$(addprefix Doxygen/wiki/,$(WIKI))) \
+	lib/ProtocolBuffers/arangodb.pb.h \
+	arangod/Ahuacatl/ahuacatl-grammar.h bin/arango-password \
+	bin/arango-upgrade bin/arango-dfdb $(DOXYGEN) $(addsuffix \
+	.md,$(addprefix Doxygen/xml/,$(WIKI))) $(addsuffix \
+	.md,$(addprefix Doxygen/wiki/,$(WIKI))) \
 	Doxygen/.setup-directories $(JAVASCRIPT_HEADER) \
 	.setup-js-directories $(am__append_17) $(am__append_20) \
 	$(am__append_22) $(PROTOBUF_FILES) $(am__append_24) \
diff --git a/arangod/Ahuacatl/ahuacatl-codegen.c b/arangod/Ahuacatl/ahuacatl-codegen.c
old mode 100755
new mode 100644
diff --git a/arangod/Ahuacatl/ahuacatl-context.c b/arangod/Ahuacatl/ahuacatl-context.c
old mode 100755
new mode 100644
diff --git a/arangod/Ahuacatl/ahuacatl-grammar.y b/arangod/Ahuacatl/ahuacatl-grammar.y
old mode 100755
new mode 100644
diff --git a/arangod/Ahuacatl/ahuacatl-index.c b/arangod/Ahuacatl/ahuacatl-index.c
old mode 100755
new mode 100644
diff --git a/arangod/Ahuacatl/ahuacatl-optimiser.c b/arangod/Ahuacatl/ahuacatl-optimiser.c
old mode 100755
new mode 100644
diff --git a/arangod/Ahuacatl/ahuacatl-tokens.c b/arangod/Ahuacatl/ahuacatl-tokens.c
index dc8d6c80a2..e5da74e95f 100644
--- a/arangod/Ahuacatl/ahuacatl-tokens.c
+++ b/arangod/Ahuacatl/ahuacatl-tokens.c
@@ -53,6 +53,7 @@ typedef int flex_int32_t;
 typedef unsigned char flex_uint8_t; 
 typedef unsigned short int flex_uint16_t;
 typedef unsigned int flex_uint32_t;
+#endif /* ! C99 */
 
 /* Limits of integral types. */
 #ifndef INT8_MIN
@@ -83,8 +84,6 @@ typedef unsigned int flex_uint32_t;
 #define UINT32_MAX             (4294967295U)
 #endif
 
-#endif /* ! C99 */
-
 #endif /* ! FLEXINT_H */
 
 #ifdef __cplusplus
@@ -158,15 +157,7 @@ typedef void* yyscan_t;
 
 /* Size of default input buffer. */
 #ifndef YY_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k.
- * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
- * Ditto for the __ia64__ case accordingly.
- */
-#define YY_BUF_SIZE 32768
-#else
 #define YY_BUF_SIZE 16384
-#endif /* __ia64__ */
 #endif
 
 /* The state buf must be large enough to hold one state per character in the main buffer.
@@ -743,12 +734,7 @@ static int input (yyscan_t yyscanner );
 
 /* Amount of stuff to slurp up with each read. */
 #ifndef YY_READ_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k */
-#define YY_READ_BUF_SIZE 16384
-#else
 #define YY_READ_BUF_SIZE 8192
-#endif /* __ia64__ */
 #endif
 
 /* Copy whatever the last rule matched to the standard output. */
@@ -756,7 +742,7 @@ static int input (yyscan_t yyscanner );
 /* This used to be an fputs(), but since the string might contain NUL's,
  * we now use fwrite().
  */
-#define ECHO do { if (fwrite( yytext, yyleng, 1, yyout )) {} } while (0)
+#define ECHO fwrite( yytext, yyleng, 1, yyout )
 #endif
 
 /* Gets input and stuffs it into "buf".  number of characters read, or YY_NULL,
@@ -767,7 +753,7 @@ static int input (yyscan_t yyscanner );
 	if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
 		{ \
 		int c = '*'; \
-		size_t n; \
+		int n; \
 		for ( n = 0; n < max_size && \
 			     (c = getc( yyin )) != EOF && c != '\n'; ++n ) \
 			buf[n] = (char) c; \
@@ -2052,8 +2038,8 @@ YY_BUFFER_STATE Ahuacatl_scan_string (yyconst char * yystr , yyscan_t yyscanner)
 
 /** Setup the input buffer state to scan the given bytes. The next call to Ahuacatllex() will
  * scan from a @e copy of @a bytes.
- * @param yybytes the byte buffer to scan
- * @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes.
+ * @param bytes the byte buffer to scan
+ * @param len the number of bytes in the buffer pointed to by @a bytes.
  * @param yyscanner The scanner object.
  * @return the newly allocated buffer state object.
  */
diff --git a/arangod/Makefile.files b/arangod/Makefile.files
index cb23819846..b46713112c 100755
--- a/arangod/Makefile.files
+++ b/arangod/Makefile.files
@@ -128,6 +128,9 @@ FLEX_FILES += \
 BISON_FILES += \
 	arangod/Ahuacatl/ahuacatl-grammar.c
 
+CLEANUP += \
+	arangod/Ahuacatl/ahuacatl-grammar.h
+
 ################################################################################
 ## --SECTION--                                                       END-OF-FILE
 ################################################################################
diff --git a/lib/JsonParser/json-parser.c b/lib/JsonParser/json-parser.c
index dee02ab1b0..d5fd779efd 100644
--- a/lib/JsonParser/json-parser.c
+++ b/lib/JsonParser/json-parser.c
@@ -96,6 +96,7 @@ typedef int flex_int32_t;
 typedef unsigned char flex_uint8_t; 
 typedef unsigned short int flex_uint16_t;
 typedef unsigned int flex_uint32_t;
+#endif /* ! C99 */
 
 /* Limits of integral types. */
 #ifndef INT8_MIN
@@ -126,8 +127,6 @@ typedef unsigned int flex_uint32_t;
 #define UINT32_MAX             (4294967295U)
 #endif
 
-#endif /* ! C99 */
-
 #endif /* ! FLEXINT_H */
 
 #ifdef __cplusplus
@@ -201,15 +200,7 @@ typedef void* yyscan_t;
 
 /* Size of default input buffer. */
 #ifndef YY_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k.
- * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
- * Ditto for the __ia64__ case accordingly.
- */
-#define YY_BUF_SIZE 32768
-#else
 #define YY_BUF_SIZE 16384
-#endif /* __ia64__ */
 #endif
 
 /* The state buf must be large enough to hold one state per character in the main buffer.
@@ -662,12 +653,7 @@ static int input (yyscan_t yyscanner );
 
 /* Amount of stuff to slurp up with each read. */
 #ifndef YY_READ_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k */
-#define YY_READ_BUF_SIZE 16384
-#else
 #define YY_READ_BUF_SIZE 8192
-#endif /* __ia64__ */
 #endif
 
 /* Copy whatever the last rule matched to the standard output. */
@@ -675,7 +661,7 @@ static int input (yyscan_t yyscanner );
 /* This used to be an fputs(), but since the string might contain NUL's,
  * we now use fwrite().
  */
-#define ECHO do { if (fwrite( yytext, yyleng, 1, yyout )) {} } while (0)
+#define ECHO fwrite( yytext, yyleng, 1, yyout )
 #endif
 
 /* Gets input and stuffs it into "buf".  number of characters read, or YY_NULL,
@@ -686,7 +672,7 @@ static int input (yyscan_t yyscanner );
 	if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
 		{ \
 		int c = '*'; \
-		size_t n; \
+		int n; \
 		for ( n = 0; n < max_size && \
 			     (c = getc( yyin )) != EOF && c != '\n'; ++n ) \
 			buf[n] = (char) c; \
@@ -1691,8 +1677,8 @@ YY_BUFFER_STATE tri_jsp__scan_string (yyconst char * yystr , yyscan_t yyscanner)
 
 /** Setup the input buffer state to scan the given bytes. The next call to tri_jsp_lex() will
  * scan from a @e copy of @a bytes.
- * @param yybytes the byte buffer to scan
- * @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes.
+ * @param bytes the byte buffer to scan
+ * @param len the number of bytes in the buffer pointed to by @a bytes.
  * @param yyscanner The scanner object.
  * @return the newly allocated buffer state object.
  */
diff --git a/lib/Makefile.files b/lib/Makefile.files
index 4ad5eca928..6e7aa9ee81 100644
--- a/lib/Makefile.files
+++ b/lib/Makefile.files
@@ -225,6 +225,9 @@ FLEXXX_FILES += \
 PROTOBUF_FILES += \
 	lib/ProtocolBuffers/arangodb.pb.cpp
 
+CLEANUP += \
+	lib/ProtocolBuffers/arangodb.pb.h
+
 ## -----------------------------------------------------------------------------
 ## --SECTION--                                                       END-OF-FILE
 ## -----------------------------------------------------------------------------
diff --git a/lib/V8/v8-json.cpp b/lib/V8/v8-json.cpp
index b92e9cdedb..7cc0361b21 100644
--- a/lib/V8/v8-json.cpp
+++ b/lib/V8/v8-json.cpp
@@ -115,6 +115,7 @@ typedef int flex_int32_t;
 typedef unsigned char flex_uint8_t; 
 typedef unsigned short int flex_uint16_t;
 typedef unsigned int flex_uint32_t;
+#endif /* ! C99 */
 
 /* Limits of integral types. */
 #ifndef INT8_MIN
@@ -145,8 +146,6 @@ typedef unsigned int flex_uint32_t;
 #define UINT32_MAX             (4294967295U)
 #endif
 
-#endif /* ! C99 */
-
 #endif /* ! FLEXINT_H */
 
 /* %endif */
@@ -238,15 +237,7 @@ typedef void* yyscan_t;
 
 /* Size of default input buffer. */
 #ifndef YY_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k.
- * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
- * Ditto for the __ia64__ case accordingly.
- */
-#define YY_BUF_SIZE 32768
-#else
 #define YY_BUF_SIZE 16384
-#endif /* __ia64__ */
 #endif
 
 /* The state buf must be large enough to hold one state per character in the main buffer.
@@ -775,12 +766,7 @@ static int input (yyscan_t yyscanner );
 
 /* Amount of stuff to slurp up with each read. */
 #ifndef YY_READ_BUF_SIZE
-#ifdef __ia64__
-/* On IA-64, the buffer size is 16k, not 8k */
-#define YY_READ_BUF_SIZE 16384
-#else
 #define YY_READ_BUF_SIZE 8192
-#endif /* __ia64__ */
 #endif
 
 /* Copy whatever the last rule matched to the standard output. */
@@ -789,7 +775,7 @@ static int input (yyscan_t yyscanner );
 /* This used to be an fputs(), but since the string might contain NUL's,
  * we now use fwrite().
  */
-#define ECHO do { if (fwrite( yytext, yyleng, 1, yyout )) {} } while (0)
+#define ECHO fwrite( yytext, yyleng, 1, yyout )
 /* %endif */
 /* %if-c++-only C++ definition */
 /* %endif */
@@ -804,7 +790,7 @@ static int input (yyscan_t yyscanner );
 	if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
 		{ \
 		int c = '*'; \
-		size_t n; \
+		int n; \
 		for ( n = 0; n < max_size && \
 			     (c = getc( yyin )) != EOF && c != '\n'; ++n ) \
 			buf[n] = (char) c; \
@@ -1956,8 +1942,8 @@ YY_BUFFER_STATE tri_v8__scan_string (yyconst char * yystr , yyscan_t yyscanner)
 /* %if-c-only */
 /** Setup the input buffer state to scan the given bytes. The next call to tri_v8_lex() will
  * scan from a @e copy of @a bytes.
- * @param yybytes the byte buffer to scan
- * @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes.
+ * @param bytes the byte buffer to scan
+ * @param len the number of bytes in the buffer pointed to by @a bytes.
  * @param yyscanner The scanner object.
  * @return the newly allocated buffer state object.
  */