diff --git a/Makefile b/Makefile
index a5965bdf1a..a738df1545 100644
--- a/Makefile
+++ b/Makefile
@@ -2155,7 +2155,7 @@ exec_cmd.sp exec_cmd.s exec_cmd.o: GIT-PREFIX
 exec_cmd.sp exec_cmd.s exec_cmd.o: EXTRA_CPPFLAGS = \
 	'-DGIT_EXEC_PATH="$(gitexecdir_SQ)"' \
 	'-DBINDIR="$(bindir_relative_SQ)"' \
-	'-DPREFIX="$(prefix_SQ)"'
+	'-DFALLBACK_RUNTIME_PREFIX="$(prefix_SQ)"'
 
 builtin/init-db.sp builtin/init-db.s builtin/init-db.o: GIT-PREFIX
 builtin/init-db.sp builtin/init-db.s builtin/init-db.o: EXTRA_CPPFLAGS = \
@@ -2455,7 +2455,7 @@ bin-wrappers/%: wrap-for-bin.sh
 	@mkdir -p bin-wrappers
 	$(QUIET_GEN)sed -e '1s|#!.*/sh|#!$(SHELL_PATH_SQ)|' \
 	     -e 's|@@BUILD_DIR@@|$(shell pwd)|' \
-	     -e 's|@@PROG@@|$(patsubst test-%,t/helper/test-%,$(@F))|' < $< > $@ && \
+	     -e 's|@@PROG@@|$(patsubst test-%,t/helper/test-%$(X),$(@F))$(patsubst git%,$(X),$(filter $(@F),$(BINDIR_PROGRAMS_NEED_X)))|' < $< > $@ && \
 	chmod +x $@
 
 # GNU make supports exporting all variables by "export" without parameters.
diff --git a/builtin/rev-list.c b/builtin/rev-list.c
index d95acaa40e..9d8dc34758 100644
--- a/builtin/rev-list.c
+++ b/builtin/rev-list.c
@@ -479,7 +479,8 @@ int cmd_rev_list(int argc, const char **argv, const char *prefix)
 		mark_edges_uninteresting(&revs, show_edge);
 
 	if (bisect_list) {
-		int reaches = reaches, all = all;
+		FAKE_INIT(int, reaches, 0);
+		FAKE_INIT(int, all, 0);
 
 		find_bisection(&revs.commits, &reaches, &all, bisect_find_all);
 
diff --git a/compat/obstack.h b/compat/obstack.h
index 6bc24b7644..f0807eaa3b 100644
--- a/compat/obstack.h
+++ b/compat/obstack.h
@@ -492,7 +492,7 @@ __extension__								\
 ( (h)->temp.tempint = (char *) (obj) - (char *) (h)->chunk,		\
   ((((h)->temp.tempint > 0						\
     && (h)->temp.tempint < (h)->chunk_limit - (char *) (h)->chunk))	\
-   ? (int) ((h)->next_free = (h)->object_base				\
+   ? (ptrdiff_t) ((h)->next_free = (h)->object_base				\
 	    = (h)->temp.tempint + (char *) (h)->chunk)			\
    : (((obstack_free) ((h), (h)->temp.tempint + (char *) (h)->chunk), 0), 0)))
 
diff --git a/compat/terminal.c b/compat/terminal.c
index 1d37f0aafb..d9d3945afa 100644
--- a/compat/terminal.c
+++ b/compat/terminal.c
@@ -1,4 +1,6 @@
+#ifndef NO_INTTYPES_H
 #include <inttypes.h>
+#endif
 #include "git-compat-util.h"
 #include "run-command.h"
 #include "compat/terminal.h"
diff --git a/config.mak.uname b/config.mak.uname
index c263449b90..928f88d671 100644
--- a/config.mak.uname
+++ b/config.mak.uname
@@ -392,6 +392,9 @@ ifeq ($(uname_S),Windows)
 		compat/win32/dirent.o compat/win32/fscache.o
 	COMPAT_CFLAGS = -D__USE_MINGW_ACCESS -DDETECT_MSYS_TTY -DNOGDI -DHAVE_STRING_H -Icompat -Icompat/regex -Icompat/win32 -DSTRIP_EXTENSION=\".exe\"
 	BASIC_LDFLAGS = -IGNORE:4217 -IGNORE:4049 -NOLOGO -SUBSYSTEM:CONSOLE
+	# invalidcontinue.obj allows Git's source code to close the same file
+	# handle twice, or to access the osfhandle of an already-closed stdout
+	# See https://msdn.microsoft.com/en-us/library/ms235330.aspx
 	EXTLIBS = user32.lib advapi32.lib shell32.lib wininet.lib ws2_32.lib invalidcontinue.obj kernel32.lib ntdll.lib
 	PTHREAD_LIBS =
 	lib =
diff --git a/exec_cmd.c b/exec_cmd.c
index ce192a2d64..978af936f7 100644
--- a/exec_cmd.c
+++ b/exec_cmd.c
@@ -20,7 +20,7 @@ static const char *system_prefix(void)
 	    !(prefix = strip_path_suffix(argv0_path, GIT_EXEC_PATH)) &&
 	    !(prefix = strip_path_suffix(argv0_path, BINDIR)) &&
 	    !(prefix = strip_path_suffix(argv0_path, "git"))) {
-		prefix = PREFIX;
+		prefix = FALLBACK_RUNTIME_PREFIX;
 		trace_printf("RUNTIME_PREFIX requested, "
 				"but prefix computation failed.  "
 				"Using static fallback '%s'.\n", prefix);
@@ -45,7 +45,7 @@ void git_extract_argv0_path(const char *argv0)
 
 static const char *system_prefix(void)
 {
-	return PREFIX;
+	return FALLBACK_RUNTIME_PREFIX;
 }
 
 void git_extract_argv0_path(const char *argv0)
diff --git a/fast-import.c b/fast-import.c
index b70ac025e0..04023e7c5f 100644
--- a/fast-import.c
+++ b/fast-import.c
@@ -3003,7 +3003,7 @@ static void cat_blob(struct object_entry *oe, struct object_id *oid)
 
 static void parse_get_mark(const char *p)
 {
-	struct object_entry *oe = oe;
+	FAKE_INIT(struct object_entry *, oe, NULL);
 	char output[GIT_MAX_HEXSZ + 2];
 
 	/* get-mark SP <object> LF */
@@ -3020,7 +3020,7 @@ static void parse_get_mark(const char *p)
 
 static void parse_cat_blob(const char *p)
 {
-	struct object_entry *oe = oe;
+	FAKE_INIT(struct object_entry *, oe, NULL);
 	struct object_id oid;
 
 	/* cat-blob SP <object> LF */
diff --git a/git-compat-util.h b/git-compat-util.h
index bbd92a8627..6069a4bffb 100644
--- a/git-compat-util.h
+++ b/git-compat-util.h
@@ -51,6 +51,23 @@
 #endif
 #endif
 
+/*
+ * Under certain circumstances Git's source code is cleverer than the C
+ * compiler when the latter warns about some "uninitialized value", e.g. when
+ * a value is both initialized and used under the same condition.
+ *
+ * GCC can be fooled to not spit out this warning by using the construct:
+ * "int value = value;". Other C compilers are not that easily fooled and would
+ * require a #pragma (which is not portable, and would litter the source code).
+ *
+ * To keep things simple, we only fool GCC, and initialize such values instead
+ * when compiling with other C compilers.
+ */
+#ifdef __GNUC__
+#define FAKE_INIT(a, b, c) a b = b
+#else
+#define FAKE_INIT(a, b, c) a b = c
+#endif
 
 /*
  * BUILD_ASSERT_OR_ZERO - assert a build-time dependency, as an expression.
diff --git a/merge-recursive.c b/merge-recursive.c
index cc5fa0a949..12c968eeaa 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -2070,7 +2070,7 @@ int merge_recursive(struct merge_options *o,
 {
 	struct commit_list *iter;
 	struct commit *merged_common_ancestors;
-	struct tree *mrtree = mrtree;
+	FAKE_INIT(struct tree *, mrtree, NULL);
 	int clean;
 
 	if (show(o, 4)) {
diff --git a/perl/Makefile b/perl/Makefile
index f657de20e3..cf2f699362 100644
--- a/perl/Makefile
+++ b/perl/Makefile
@@ -22,7 +22,9 @@ clean:
 	$(RM) $(makfile).old
 	$(RM) PM.stamp
 
+ifneq (,$(wildcard PM.stamp))
 $(makfile): PM.stamp
+endif
 
 ifdef NO_PERL_MAKEMAKER
 instdir_SQ = $(subst ','\'',$(prefix)/lib)
diff --git a/read-cache.c b/read-cache.c
index 198e72b685..0e41ceac36 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -2104,7 +2104,7 @@ static int ce_write_entry(git_SHA_CTX *c, int fd, struct cache_entry *ce,
 			  struct strbuf *previous_name, struct ondisk_cache_entry *ondisk)
 {
 	int size;
-	int saved_namelen = saved_namelen; /* compiler workaround */
+	FAKE_INIT(int, saved_namelen, 0);
 	int result;
 	static unsigned char padding[8] = { 0x00 };
 
diff --git a/sideband.c b/sideband.c
index 6d7f943e43..325bf0e974 100644
--- a/sideband.c
+++ b/sideband.c
@@ -13,7 +13,7 @@
  * the remote died unexpectedly.  A flush() concludes the stream.
  */
 
-#define PREFIX "remote: "
+#define DISPLAY_PREFIX "remote: "
 
 #define ANSI_SUFFIX "\033[K"
 #define DUMB_SUFFIX "        "
@@ -49,7 +49,7 @@ int recv_sideband(const char *me, int in_stream, int out)
 		switch (band) {
 		case 3:
 			strbuf_addf(&outbuf, "%s%s%s", outbuf.len ? "\n" : "",
-				    PREFIX, buf + 1);
+				    DISPLAY_PREFIX, buf + 1);
 			retval = SIDEBAND_REMOTE_ERROR;
 			break;
 		case 2:
@@ -67,7 +67,7 @@ int recv_sideband(const char *me, int in_stream, int out)
 				int linelen = brk - b;
 
 				if (!outbuf.len)
-					strbuf_addstr(&outbuf, PREFIX);
+					strbuf_addstr(&outbuf, DISPLAY_PREFIX);
 				if (linelen > 0) {
 					strbuf_addf(&outbuf, "%.*s%s%c",
 						    linelen, b, suffix, *brk);
@@ -81,8 +81,8 @@ int recv_sideband(const char *me, int in_stream, int out)
 			}
 
 			if (*b)
-				strbuf_addf(&outbuf, "%s%s",
-					    outbuf.len ? "" : PREFIX, b);
+				strbuf_addf(&outbuf, "%s%s", outbuf.len ?
+					    "" : DISPLAY_PREFIX, b);
 			break;
 		case 1:
 			write_or_die(out, buf + 1, len);
diff --git a/t/t5505-remote.sh b/t/t5505-remote.sh
index a6c0178f3a..f14afab5dd 100755
--- a/t/t5505-remote.sh
+++ b/t/t5505-remote.sh
@@ -830,6 +830,7 @@ test_expect_success 'migrate a remote from named file in $GIT_DIR/branches' '
 	(
 		cd six &&
 		git remote rm origin &&
+		mkdir -p .git/branches &&
 		echo "$origin_url" >.git/branches/origin &&
 		git remote rename origin origin &&
 		test_path_is_missing .git/branches/origin &&
@@ -844,6 +845,7 @@ test_expect_success 'migrate a remote from named file in $GIT_DIR/branches (2)'
 	(
 		cd seven &&
 		git remote rm origin &&
+		mkdir -p .git/branches &&
 		echo "quux#foom" > .git/branches/origin &&
 		git remote rename origin origin &&
 		test_path_is_missing .git/branches/origin &&
diff --git a/t/t5516-fetch-push.sh b/t/t5516-fetch-push.sh
index 177897ea0b..457f648ad9 100755
--- a/t/t5516-fetch-push.sh
+++ b/t/t5516-fetch-push.sh
@@ -866,6 +866,7 @@ test_expect_success 'fetch with branches' '
 	mk_empty testrepo &&
 	git branch second $the_first_commit &&
 	git checkout second &&
+	mkdir -p testrepo/.git/branches &&
 	echo ".." > testrepo/.git/branches/branch1 &&
 	(
 		cd testrepo &&
@@ -879,6 +880,7 @@ test_expect_success 'fetch with branches' '
 
 test_expect_success 'fetch with branches containing #' '
 	mk_empty testrepo &&
+	mkdir -p testrepo/.git/branches &&
 	echo "..#second" > testrepo/.git/branches/branch2 &&
 	(
 		cd testrepo &&
@@ -893,6 +895,7 @@ test_expect_success 'fetch with branches containing #' '
 test_expect_success 'push with branches' '
 	mk_empty testrepo &&
 	git checkout second &&
+	mkdir -p .git/branches &&
 	echo "testrepo" > .git/branches/branch1 &&
 	git push branch1 &&
 	(
@@ -905,6 +908,7 @@ test_expect_success 'push with branches' '
 
 test_expect_success 'push with branches containing #' '
 	mk_empty testrepo &&
+	mkdir -p .git/branches &&
 	echo "testrepo#branch3" > .git/branches/branch2 &&
 	git push branch2 &&
 	(