I think the real bug is that unlink(), rename() and rmdir() 
don't refresh the related realpath cache entries.

Here's a patch that fixes this, also available from ftp://
ftp.c9x.org/misc/
php_sync_realpath_cache_with_unlink_and_rename.diff



--- TSRM/tsrm_virtual_cwd.c.orig        Sat Nov  4 00:56:05 
2006
+++ TSRM/tsrm_virtual_cwd.c     Sat Nov  4 02:53:13 2006
@@ -361,6 +361,23 @@
 }
 
 
+CWD_API int realpath_cache_delete(const char *path, int 
path_len) {
+       unsigned long key = realpath_cache_key(path, 
path_len);
+       unsigned long n = key % (sizeof(CWDG
(realpath_cache)) / sizeof(CWDG(realpath_cache)[0]));
+       realpath_cache_bucket **bucket = &CWDG
(realpath_cache)[n];
+
+       while (*bucket != NULL) {
+               if (key == (*bucket)->key && path_len == 
(*bucket)->path_len &&
+                          memcmp(path, (*bucket)->path, 
path_len) == 0) {
+                       realpath_cache_bucket *r = *bucket;
+                       *bucket = (*bucket)->next;
+                       CWDG(realpath_cache_size) -= sizeof
(realpath_cache_bucket) + r->path_len + 1 + r->realpath_len 
+ 1;
+                       free(r);
+               }
+       }
+       return 0;
+}
+
 /* Resolve path relatively to state and put the real path 
into state */
 /* returns 0 for ok, 1 for error */
 CWD_API int virtual_file_ex(cwd_state *state, const char 
*path, verify_path_func verify_path, int use_realpath)
--- TSRM/tsrm_virtual_cwd.h.orig        Sat Nov  4 02:39:04 
2006
+++ TSRM/tsrm_virtual_cwd.h     Sat Nov  4 02:48:04 2006
@@ -232,14 +232,14 @@
 #define VCWD_CHDIR_FILE(path) virtual_chdir_file(path, 
virtual_chdir TSRMLS_CC)
 #define VCWD_GETWD(buf)
 #define VCWD_REALPATH(path, real_path) virtual_realpath
(path, real_path TSRMLS_CC)
-#define VCWD_RENAME(oldname, newname) virtual_rename
(oldname, newname TSRMLS_CC)
+#define VCWD_RENAME(oldname, newname) (virtual_rename
(oldname, newname TSRMLS_CC) + realpath_cache_delete
(oldname, strlen(oldname)) + realpath_cache_delete(newname, 
strlen(newname)))
 #define VCWD_STAT(path, buff) virtual_stat(path, buff 
TSRMLS_CC)
 #if !defined(TSRM_WIN32)
 #define VCWD_LSTAT(path, buff) virtual_lstat(path, buff 
TSRMLS_CC)
 #endif
-#define VCWD_UNLINK(path) virtual_unlink(path TSRMLS_CC)
+#define VCWD_UNLINK(path) (virtual_unlink(path TSRMLS_CC) + 
realpath_cache_delete(path, strlen(path)))
 #define VCWD_MKDIR(pathname, mode) virtual_mkdir(pathname, 
mode TSRMLS_CC)
-#define VCWD_RMDIR(pathname) virtual_rmdir(pathname 
TSRMLS_CC)
+#define VCWD_RMDIR(pathname) (virtual_rmdir(pathname 
TSRMLS_CC) + realpath_cache_delete(pathname, strlen
(pathname)))
 #define VCWD_OPENDIR(pathname) virtual_opendir(pathname 
TSRMLS_CC)
 #define VCWD_POPEN(command, type) virtual_popen(command, 
type TSRMLS_CC)
 #define VCWD_ACCESS(pathname, mode) virtual_access
(pathname, mode TSRMLS_CC)
@@ -261,15 +261,15 @@
 #define VCWD_OPEN(path, flags) open(path, flags)
 #define VCWD_OPEN_MODE(path, flags, mode)      open(path, 
flags, mode)
 #define VCWD_CREAT(path, mode) creat(path, mode)
-#define VCWD_RENAME(oldname, newname) rename(oldname, 
newname)
+#define VCWD_RENAME(oldname, newname) (rename(oldname, 
newname) + realpath_cache_delete(oldname, strlen(oldname)) + 
realpath_cache_delete(newname, strlen(newname)))
 #define VCWD_CHDIR(path) chdir(path)
 #define VCWD_CHDIR_FILE(path) virtual_chdir_file(path, 
chdir)
 #define VCWD_GETWD(buf) getwd(buf)
 #define VCWD_STAT(path, buff) stat(path, buff)
 #define VCWD_LSTAT(path, buff) lstat(path, buff)
-#define VCWD_UNLINK(path) unlink(path)
+#define VCWD_UNLINK(path) (unlink(path) + 
realpath_cache_delete(path, strlen(path)))
 #define VCWD_MKDIR(pathname, mode) mkdir(pathname, mode)
-#define VCWD_RMDIR(pathname) rmdir(pathname)
+#define VCWD_RMDIR(pathname) (rmdir(pathname) + 
realpath_cache_delete(pathname, strlen(pathname)))
 #define VCWD_OPENDIR(pathname) opendir(pathname)
 #define VCWD_POPEN(command, type) popen(command, type)
 #if defined(TSRM_WIN32)

Another fix is to have clearstatcache() also clear the 
realpath cache.

Patch follows. Also available from ftp://ftp.c9x.org/misc/
php_clearstatcache_should_clear_realpath_cache.diff

--- ext/standard/filestat.c.orig        Sat Nov  4 13:14:10 
2006
+++ ext/standard/filestat.c     Sat Nov  4 13:14:40 2006
@@ -633,6 +633,7 @@
                efree(BG(CurrentLStatFile));
                BG(CurrentLStatFile) = NULL;
        }
+       realpath_cache_empty();
 }
 /* }}} */
 
--- TSRM/tsrm_virtual_cwd.c.orig        Sat Nov  4 00:56:05 
2006
+++ TSRM/tsrm_virtual_cwd.c     Sat Nov  4 13:28:29 2006
@@ -360,6 +360,24 @@
        return NULL;
 }
 
+CWD_API int realpath_cache_empty(void)
+{
+       int i;
+       
+       for (i = 0; i < sizeof(CWDG(realpath_cache)) / 
sizeof(CWDG(realpath_cache)[0]); i++) {
+               realpath_cache_bucket *bucket = CWDG
(realpath_cache)[i];
+
+               while (bucket != NULL) {
+                       realpath_cache_bucket *r = bucket;
+                       bucket = bucket->next;
+                       free(r);
+               }
+               CWDG(realpath_cache)[i] = NULL;
+       }
+       CWDG(realpath_cache_size) = 0;
+       
+       return 0;
+}
 
 /* Resolve path relatively to state and put the real path 
into state */
 /* returns 0 for ok, 1 for error */
--- TSRM/tsrm_virtual_cwd.h.orig        Sat Nov  4 02:39:04 
2006
+++ TSRM/tsrm_virtual_cwd.h     Sat Nov  4 13:12:50 2006
@@ -156,6 +156,7 @@
 CWD_API DIR *virtual_opendir(const char *pathname 
TSRMLS_DC);
 CWD_API FILE *virtual_popen(const char *command, const char 
*type TSRMLS_DC);
 CWD_API int virtual_access(const char *pathname, int mode 
TSRMLS_DC);
+CWD_API int realpath_cache_empty(void);
 #if defined(TSRM_WIN32)
 /* these are not defined in win32 headers */
 #ifndef W_OK

The last patch is applied, so you have to use clearstatcache().

rename() and unlink() may rename/unlink directory and it may break several nested entries from realpath cache.

Fixed in CVS HEAD and PHP_5_2.

Thank you!

-Frank.