relase 0.3

--copy-always
--sort
bi-directory merges
--check-md


git-svn-id: file:///home/lennart/svn/public/syrep/trunk@43 07ea20a6-d2c5-0310-9e02-9ef735347d72

23 files changed, 328 insertions, 88 deletions

diff --git a/src/cache.c b/src/cache.c
index 925cd69..6722b55 100644
--- a/src/cache.c
+++ b/src/cache.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <db.h>
 #include <stdlib.h>
 #include <assert.h>
@@ -157,7 +161,7 @@ int md_cache_get(struct syrep_md_cache *c, const char *path, uint8_t digest[16])
     struct stat st;
     
     if ((fd = open(path, O_RDONLY)) < 0) {
-        fprintf(stderr, "open(%s): %s\n", path, strerror(errno));
+        fprintf(stderr, "open(\"%s\"): %s\n", path, strerror(errno));
         goto finish;
     }
     
diff --git a/src/cleanup.c b/src/cleanup.c
index 6f096f9..447697d 100644
--- a/src/cleanup.c
+++ b/src/cleanup.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <unistd.h>
 #include <string.h>
 #include <limits.h>
diff --git a/src/context.c b/src/context.c
index 677704d..9fe37bb 100644
--- a/src/context.c
+++ b/src/context.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdlib.h>
 #include <string.h>
 #include <assert.h>
diff --git a/src/dbstruct.h b/src/dbstruct.h
index 74c6059..842e33d 100644
--- a/src/dbstruct.h
+++ b/src/dbstruct.h
@@ -59,7 +59,7 @@ struct syrep_nhash {                     /* name hash */
 };
 
 struct syrep_name {
-    char path[PATH_MAX+1];
+    char path[PATH_MAX];
 };
 
 
@@ -69,11 +69,11 @@ struct syrep_name {
  * syrep_md :: syrep_nrecno         => md_nrecno                           (DUP)
  * syrep_nrecno :: syrep_md         => nrecno_md                           (DUP)
  * syrep_nrecno :: syrep_md         => nrecno_lastmd
- * syrep_md :: syrep_nrecono        => md_lastnrecno
+ * syrep_md :: syrep_nrecno         => md_lastnrecno
  *
  * syrep_version :: syrep_timestamp => version_timestamp
  *
- * nhash :: nrecno                  => nhash_nrecno                          (DUP)
+ * nhash :: nrecno                  => nhash_nrecno                        (DUP)
  * nrecno :: name                   => nrecno_name
  */
 
diff --git a/src/dbutil.c b/src/dbutil.c
index d7aa319..cfa3150 100644
--- a/src/dbutil.c
+++ b/src/dbutil.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <string.h>
 #include <assert.h>
 #include <time.h>
@@ -152,6 +156,14 @@ int get_current_md_by_nrecno(struct syrep_db_context *c, const struct syrep_nrec
     return 1;
 }
 
+int get_current_md_by_name(struct syrep_db_context *c, const struct syrep_name *name, struct syrep_md *md) {
+    struct syrep_nrecno nrecno;
+
+    if (get_nrecno_by_name(c, name, &nrecno, 0) < 0)
+        return -1;
+
+    return get_current_md_by_nrecno(c, &nrecno, md);
+}
 
 uint32_t get_version_timestamp(struct syrep_db_context *c, uint32_t v) {
     DBT key, data;
@@ -210,7 +222,8 @@ int get_name_by_nrecno(struct syrep_db_context *c, const struct syrep_nrecno *nr
 
     if (name) {
         memset(name, 0, sizeof(struct syrep_name));
-        strncpy(name->path, data.data, MIN(PATH_MAX, data.size));
+        strncpy(name->path, data.data, MIN(PATH_MAX-1, data.size));
+        name->path[PATH_MAX-1] = 0;
     }
 
     return 1;
diff --git a/src/dbutil.h b/src/dbutil.h
index dd4acd2..9d9837c 100644
--- a/src/dbutil.h
+++ b/src/dbutil.h
@@ -27,6 +27,7 @@
 int get_meta_by_nrecno_md(struct syrep_db_context *c, const struct syrep_nrecno*nrecno, const struct syrep_md *md, struct syrep_meta *meta);
 int get_last_md_by_nrecno(struct syrep_db_context *c, const struct syrep_nrecno *nrecno, struct syrep_md *md);
 int get_current_md_by_nrecno(struct syrep_db_context *c, const struct syrep_nrecno *nrecno, struct syrep_md *md);
+int get_current_md_by_name(struct syrep_db_context *c, const struct syrep_name *name, struct syrep_md *md);
 int get_current_nrecno_by_md(struct syrep_db_context *c, const struct syrep_md *md, struct syrep_nrecno *nrecno);
 uint32_t get_version_timestamp(struct syrep_db_context *c, uint32_t v);
 
diff --git a/src/diff.c b/src/diff.c
index 9a87d81..a589504 100644
--- a/src/diff.c
+++ b/src/diff.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <assert.h>
 #include <string.h>
 #include <stdlib.h>
diff --git a/src/dump.c b/src/dump.c
index 289478b..5a9b721 100644
--- a/src/dump.c
+++ b/src/dump.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdio.h>
 #include <assert.h>
 #include <string.h>
diff --git a/src/extract.c b/src/extract.c
index ec1d8f0..2e63d14 100644
--- a/src/extract.c
+++ b/src/extract.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdlib.h>
 #include <fcntl.h>
 #include <unistd.h>
diff --git a/src/history.c b/src/history.c
index 4da91d5..ff8532e 100644
--- a/src/history.c
+++ b/src/history.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <assert.h>
 #include <string.h>
 #include <time.h>
diff --git a/src/info.c b/src/info.c
index 14446c2..a35877c 100644
--- a/src/info.c
+++ b/src/info.c
@@ -18,16 +18,22 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdio.h>
 #include <assert.h>
+#include <time.h>
 
 #include "info.h"
 #include "util.h"
 
 int info(struct syrep_db_context *c) {
+    time_t t = (time_t) c->timestamp;
     assert(c);
     fprintf(stdout, "Origin: %s\n", c->origin);
-    fprintf(stdout, "Timestamp: %u; %s", c->timestamp, asctime(localtime(&c->timestamp)));
+    fprintf(stdout, "Timestamp: %u; %s", c->timestamp, asctime(localtime(&t)));
     fprintf(stdout, "Version: %u\n", c->version);
     fprintf(stdout, "Database nrecno_meta: ");
     statistics(c->db_id_meta);
diff --git a/src/list.c b/src/list.c
index e5fe62f..f1763eb 100644
--- a/src/list.c
+++ b/src/list.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <string.h>
 #include <assert.h>
 #include <stdlib.h>
@@ -30,17 +34,21 @@
 #include "dbutil.h"
 #include "syrep.h"
 
-static int handle_file(struct syrep_db_context *c, const struct syrep_nrecno *nrecno, const struct syrep_md *md, const struct syrep_meta *meta) {
+static int handle_file(struct syrep_db_context *c, const struct syrep_nrecno *nrecno, const struct syrep_md *md, const struct syrep_meta *meta, const struct syrep_name *name) {
     struct syrep_meta local_meta;
-    struct syrep_name name;
-    int f;
+    struct syrep_name local_name;
     
     assert(c && nrecno && md);
 
-    if ((f = get_name_by_nrecno(c, nrecno, &name)) < 0)
-        return -1;
+    if (!name) {
+        int f;
+    
+        if ((f = get_name_by_nrecno(c, nrecno, &local_name)) < 0)
+            return -1;
 
-    assert(f);
+        assert(f);
+        name = &local_name;
+    }
     
     if (!meta) {
         int f;
@@ -60,9 +68,9 @@ static int handle_file(struct syrep_db_context *c, const struct syrep_nrecno *nr
             fhex(md->digest, SYREP_DIGESTLENGTH, d);
             d[SYREP_DIGESTLENGTH*2] = 0;
             
-            printf("%s %s%s", d, name.path, meta->last_seen == c->version ? "\t\t" : "\t(deleted)");
+            printf("%s %s%s", d, name->path, meta->last_seen == c->version ? "\t\t" : "\t(deleted)");
         } else
-            printf("\t%s%s", name.path, meta->last_seen == c->version ? "\t\t" : "\t(deleted)");
+            printf("\t%s%s", name->path, meta->last_seen == c->version ? "\t\t" : "\t(deleted)");
         
         if (args.show_times_flag)
             printf( "\t(first-seen: %u; last-seen: %u)\n", meta->first_seen, meta->last_seen);
@@ -73,16 +81,44 @@ static int handle_file(struct syrep_db_context *c, const struct syrep_nrecno *nr
         fhex(md->digest, SYREP_DIGESTLENGTH, d);
         d[SYREP_DIGESTLENGTH*2] = 0;
         
-        printf("\t%s", name.path);
+        printf("\t%s", name->path);
     }
             
     return 0;
 }
 
+struct sort_entry {
+    struct syrep_nrecno nrecno;
+    struct syrep_md md;
+    struct syrep_meta meta;
+    struct syrep_name name;
+};
+
+static int sort_entry_cmp(const void *_a, const void *_b) {
+    const struct sort_entry *a = _a, *b = _b;
+    assert(a && b);
+
+    if (a->meta.last_seen < b->meta.last_seen)
+        return -1;
+
+    if (a->meta.last_seen > b->meta.last_seen)
+        return 1;
+
+    if (a->meta.first_seen < b->meta.first_seen)
+        return -1;
+
+    if (a->meta.first_seen > b->meta.first_seen)
+        return 1;
+
+    return strncmp(a->name.path, b->name.path, PATH_MAX);
+};
+
 int list(struct syrep_db_context *c) {
     int r = -1, ret;
     DBC *cursor = NULL;
     DBT key, data;
+    struct sort_entry *sort_array = NULL;
+    unsigned n_sort_array = 0, m_sort_array = 0;
 
     if (args.show_by_md_flag) {
         struct syrep_md previous_md;
@@ -112,7 +148,7 @@ int list(struct syrep_db_context *c) {
             if ((ret = get_meta_by_nrecno_md(c, recno, md, &meta)) < 0)
                 goto finish;
 
-            if (handle_file(c, recno, md, &meta) < 0)
+            if (handle_file(c, recno, md, &meta, NULL) < 0)
                 fprintf(stderr, "handle_file() failed\n");
         }
         
@@ -123,7 +159,7 @@ int list(struct syrep_db_context *c) {
     
         r = 0;
     } else {
-
+        
         if ((ret = c->db_id_meta->cursor(c->db_id_meta, NULL, &cursor, 0)) != 0) {
             c->db_id_meta->err(c->db_id_meta, ret, "id_meta");
             goto finish;
@@ -135,9 +171,59 @@ int list(struct syrep_db_context *c) {
         while ((ret = cursor->c_get(cursor, &key, &data, DB_NEXT)) == 0) {
             struct syrep_id *id = (struct syrep_id*) key.data;
             
-            if (handle_file(c, &id->nrecno, &id->md, (struct syrep_meta*) data.data) < 0)
-                fprintf(stderr, "handle_file() failed\n");
-            
+            if (!args.sort_flag) {
+                if (handle_file(c, &id->nrecno, &id->md, (struct syrep_meta*) data.data, NULL) < 0)
+                    fprintf(stderr, "handle_file() failed\n");
+                
+            } else {
+                if (n_sort_array >= m_sort_array) {
+
+                    if (!m_sort_array) {
+                        DB_BTREE_STAT *statp;
+                        int ret;
+                        
+                        if ((ret = c->db_id_meta->stat(c->db_id_meta, &statp, 0)) != 0)
+                            break;
+
+                        m_sort_array = statp->bt_ndata;
+                        free(statp);
+                    } else
+                        m_sort_array *= 2;
+
+                    sort_array = realloc(sort_array, m_sort_array * sizeof(struct sort_entry));
+                }
+
+                assert(n_sort_array < m_sort_array);
+                
+                if (get_name_by_nrecno(c, &id->nrecno, &sort_array[n_sort_array].name) != 1)
+                    goto finish;
+
+                memcpy(&sort_array[n_sort_array].nrecno, &id->nrecno, sizeof(struct syrep_nrecno));
+                memcpy(&sort_array[n_sort_array].md, &id->md, sizeof(struct syrep_md));
+                memcpy(&sort_array[n_sort_array].meta, data.data, sizeof(struct syrep_meta));
+                n_sort_array++;
+            }
+
+            if (interrupted) {
+                fprintf(stderr, "Canceled.\n");
+                goto finish;
+            }
+        }
+
+        if (args.sort_flag && sort_array) {
+            unsigned i;
+            struct sort_entry *se;
+            qsort(sort_array, n_sort_array, sizeof(struct sort_entry), sort_entry_cmp);
+
+            for (i = 0, se = sort_array; i < n_sort_array; i++, se++) {
+                if ((handle_file(c, &se->nrecno, &se->md, &se->meta, &se->name)) < 0)
+                    fprintf(stderr, "handle_file() failed\n");
+
+                if (interrupted) {
+                    fprintf(stderr, "Canceled.\n");
+                    goto finish;
+                }
+            }
         }
         
         if (ret != DB_NOTFOUND) {
@@ -153,5 +239,8 @@ finish:
     if (cursor)
         cursor->c_close(cursor);
 
+    if (sort_array)
+        free(sort_array);
+
     return r;
 }
diff --git a/src/makepatch.c b/src/makepatch.c
index 3de8860..bbce369 100644
--- a/src/makepatch.c
+++ b/src/makepatch.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <assert.h>
 #include <unistd.h>
 #include <string.h>
@@ -38,7 +42,7 @@ static int cb(DB *ddb, struct syrep_name *name, struct diff_entry *de, void *p)
     struct cb_info *cb_info = p;
     struct syrep_md md;
     struct syrep_nrecno nrecno;
-    char path[PATH_MAX+1];
+    char path[PATH_MAX];
     char d[SYREP_DIGESTLENGTH*2+1];
     int f, k;
 
diff --git a/src/md5.c b/src/md5.c
index 2c9c2fc..f294588 100644
--- a/src/md5.c
+++ b/src/md5.c
@@ -51,6 +51,10 @@
   1999-05-03 lpd Original version.
  */
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "md5.h"
 #include <string.h>
 
diff --git a/src/md5util.c b/src/md5util.c
index 6b9a1e2..27c6dd3 100644
--- a/src/md5util.c
+++ b/src/md5util.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <unistd.h>
 #include <sys/mman.h>
 #include <stdio.h>
@@ -25,12 +29,13 @@
 #include <string.h>
 #include <errno.h>
 #include <sys/stat.h>
+#include <fcntl.h>
 
 #include "md5util.h"
 #include "md5.h"
 #include "syrep.h"
 
-void fhex(const unsigned char *bin,int len, char *txt) {
+void fhex(const unsigned char *bin, int len, char *txt) {
     const static char hex[] = "0123456789abcdef";
     int i;
 
@@ -43,7 +48,7 @@ void fhex(const unsigned char *bin,int len, char *txt) {
 #define MMAPSIZE (100*1024*1024)
 #define BUFSIZE (1024*1024)
 
-int fdmd5(int fd, size_t l, char *md) {
+int fdmd5(int fd, off_t l, char *md) {
     void *d;
     off_t o = 0;
     size_t m;
@@ -59,6 +64,9 @@ int fdmd5(int fd, size_t l, char *md) {
         goto finish;
     }
 
+    if (l == (off_t) -1)
+        l = pre.st_size;
+    
     if (l > BUFSIZE) {
     
         m = l < MMAPSIZE ? l : MMAPSIZE;
@@ -127,3 +135,21 @@ finish:
     
     return r;
 }
+
+int fmd5(const char *fn, char *md) {
+    int fd = -1, r = -1;
+    
+    if ((fd = open(fn, O_RDONLY)) < 0) {
+        fprintf(stderr, "open(\"%s\"): %s\n", fn, strerror(errno));
+        goto finish;
+    }
+
+    r = fdmd5(fd, (off_t) -1, md);
+
+finish:
+
+    if (fd >= 0)
+        close(fd);
+
+    return r;
+}
diff --git a/src/md5util.h b/src/md5util.h
index f5a342a..373d0b8 100644
--- a/src/md5util.h
+++ b/src/md5util.h
@@ -26,6 +26,8 @@
 void fhex(const unsigned char *bin, int len, char *txt);
 #define fhex_md5(bin,txt) fhex((bin),16,(txt))
 
-int fdmd5(int fd, size_t l, char *md);
+int fdmd5(int fd, off_t l, char *md);
+
+int fmd5(const char *fn, char *md);
 
 #endif
diff --git a/src/merge.c b/src/merge.c
index 5741d83..c095f1f 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdio.h>
 #include <assert.h>
 #include <string.h>
@@ -35,10 +39,11 @@
 #include "util.h"
 
 struct cb_info {
-    struct syrep_db_context *c1;
-    struct syrep_db_context *c2;
-    const char *root;
-    char trash_dir[PATH_MAX+1];
+    struct syrep_db_context *c1; /* remote */
+    struct syrep_db_context *c2; /* local */
+    const char *root;  /* directory wherein to merge files */
+    const char *sroot;  /* An optional source directory for bi-directory merges */
+    char trash_dir[PATH_MAX];
 };
 
 static int conflict_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de, void *p) {
@@ -47,7 +52,7 @@ static int conflict_phase(DB *ddb, struct syrep_name *name, struct diff_entry *d
     struct syrep_nrecno nrecno1, nrecno2;
     int writeback = 0;
     int f1, f2;
-    char path[PATH_MAX+1];
+    char path[PATH_MAX];
 
     assert(ddb && name && de && p);
 
@@ -172,10 +177,13 @@ static int copy_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de, v
     struct syrep_name name2;
     struct syrep_nrecno nrecno, nrecno2;
     struct syrep_md md;
-    char path[PATH_MAX+1];
+    char path[PATH_MAX];
     int f;
     char d[SYREP_DIGESTLENGTH*2+1];
 
+    int (*copy_proc) (const char *, const char*, int c) = args.always_copy_flag ? copy_file : copy_or_link_file;
+        
+
     assert(ddb && name && de && p);
 
     if (de->action != DIFF_COPY && de->action != DIFF_REPLACE)
@@ -209,7 +217,7 @@ static int copy_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de, v
             return -1;
     
     if (f) {
-        char path2[PATH_MAX+1];
+        char path2[PATH_MAX];
         snprintf(path2, sizeof(path2), "%s/%s", cb_info->root, name2.path);
 
         if (args.verbose_flag)
@@ -219,7 +227,7 @@ static int copy_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de, v
             return -1;
 
         if (!access(path2, R_OK)) {
-            if (copy_or_link_file(path2, path, 0) < 0)
+            if (copy_proc(path2, path, 0) < 0)
                 return -1;
         } else {
             unsigned l;
@@ -229,27 +237,39 @@ static int copy_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de, v
             escape_path(name2.path, path2+l, sizeof(path2)-l);
 
             if (!access(path2, R_OK)) {
-                if (copy_or_link_file(path2, path, de->action == DIFF_REPLACE) < 0)
+                if (copy_proc(path2, path, de->action == DIFF_REPLACE) < 0)
                     return -1;
             } else
                 fprintf(stderr, "COPY: Local file <%s> vanished. Snapshot not up to date.\n", name2.path);
         }
         
     } else {
+        char spath[PATH_MAX];
         const char* a;
+        const char* t;
         int k;
 
         if ((k = package_get_item(cb_info->c1->package, d, 0, &a)) < 0)
             return -1;
 
+        t = "patch";
+        
+        if (!k && cb_info->sroot) {
+            snprintf(spath, sizeof(spath), "%s/%s", cb_info->sroot, name->path);
+            a = spath;
+
+            if ((k = (access(spath, R_OK) == 0)))
+                t = "tree";
+        }
+        
         if (k) {
             if (args.verbose_flag)
-                fprintf(stderr, "COPY: Copying file <%s> from patch.\n", name->path);
+                fprintf(stderr, "COPY: Copying file <%s> from %s.\n", name->path, t);
             
             if (makeprefixpath(path, 0777) < 0)
                 return -1;
             
-            if (copy_or_link_file(a, path, de->action == DIFF_REPLACE) < 0)
+            if (copy_proc(a, path, de->action == DIFF_REPLACE) < 0)
                 return -1;
         } else
             if (args.verbose_flag)
@@ -261,17 +281,43 @@ static int copy_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de, v
 
 static int delete_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de, void *p) {
     struct cb_info *cb_info = p;
-    char path[PATH_MAX+1], target[PATH_MAX+1];
+    char path[PATH_MAX], target[PATH_MAX];
     unsigned l;
 
     assert(ddb && name && de && p);
     
-    if (de->action != DIFF_DELETE)
+    if (de->action != DIFF_DELETE && de->action != DIFF_REPLACE)
+        return 0;
+
+    if (de->action == DIFF_DELETE && de->repository == cb_info->c1)
         return 0;
 
-    if (de->repository == cb_info->c1)
+    if (de->action == DIFF_REPLACE && de->repository == cb_info->c2)
         return 0;
 
+    snprintf(path, sizeof(path), "%s/%s", cb_info->root, name->path);
+
+    if (args.check_md_flag) {
+        uint8_t digest[16];
+        struct syrep_md md;
+        
+        if (fmd5(path, digest) < 0) {
+            fprintf(stderr, "Unable to calculate message digest sum on '%s'\n", name->path);
+            return -1;
+        }
+
+        if (get_current_md_by_name(cb_info->c2,
+                                   name, &md) < 0) {
+            fprintf(stderr, "Failed to get current MD by name of '%s'\n", name->path);
+            return -1;
+        }
+
+        if (memcmp(md.digest, digest, 16) != 0) {
+            fprintf(stderr, "Message digest of file to delete doesn't match snapshot data for '%s'.\n", name->path);
+            return -1;
+        }
+    }
+    
     if (args.question_flag) {
         char text[256];
         int q;
@@ -285,8 +331,6 @@ static int delete_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de,
             return 0;
     }
         
-    snprintf(path, sizeof(path), "%s/%s", cb_info->root, name->path);
-
     snprintf(target, sizeof(target), "%s/", cb_info->trash_dir);
     l = strlen(target);
     escape_path(name->path, target+l, sizeof(target)-l);
@@ -303,8 +347,9 @@ static int delete_phase(DB *ddb, struct syrep_name *name, struct diff_entry *de,
     return 0;
 }
 
-/* Merges c1 into c2 in directory "root" */
-int merge(struct syrep_db_context *c1, struct syrep_db_context *c2, const char* root) {
+/* Merges c1 into c2 in directory "root"
+ * sroot is an optional source directory, only used on bi-directory merges */
+int merge(struct syrep_db_context *c1, struct syrep_db_context *c2, const char* root, const char* sroot) {
     struct cb_info cb_info;
     DB *ddb = NULL;
     int r = -1;
@@ -313,6 +358,7 @@ int merge(struct syrep_db_context *c1, struct syrep_db_context *c2, const char*
     cb_info.c1 = c1;
     cb_info.c2 = c2;
     cb_info.root = root;
+    cb_info.sroot = sroot;
 
     snprintf(cb_info.trash_dir, sizeof(cb_info.trash_dir), "%s/.syrep/trash", root);
     mkdir_p(cb_info.trash_dir, 0777);
diff --git a/src/merge.h b/src/merge.h
index 02c1a9e..33acf11 100644
--- a/src/merge.h
+++ b/src/merge.h
@@ -23,7 +23,7 @@
 
 #include "context.h"
 
-int merge(struct syrep_db_context *c1, struct syrep_db_context *c2, const char* root);
+int merge(struct syrep_db_context *c1, struct syrep_db_context *c2, const char* root, const char* sroot);
 int empty_trash(const char *trash);
 
 #endif
diff --git a/src/package.c b/src/package.c
index 9496742..c2841ad 100644
--- a/src/package.c
+++ b/src/package.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdio.h>
 #include <inttypes.h>
 #include <stdlib.h>
diff --git a/src/syrep.c b/src/syrep.c
index e65dc1c..e063072 100644
--- a/src/syrep.c
+++ b/src/syrep.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <inttypes.h>
 #include <limits.h>
 #include <assert.h>
@@ -53,10 +57,6 @@
 #include "makepatch.h"
 #include "cleanup.h"
 
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-
 #include "svn-revision.h"
 
 volatile int interrupted = 0;
@@ -165,7 +165,7 @@ static int do_merge(void) {
     if (db_context_origin_warn(c2))
         goto finish;
     
-    if (merge(c1, c2, args.inputs[1]) < 0)
+    if (merge(c1, c2, args.inputs[1], isdirectory(args.inputs[0]) > 0 ? args.inputs[0] : NULL) < 0)
         goto finish;
 
     r = 0;
@@ -478,53 +478,58 @@ static int help(const char *argv0) {
             "Usage: %s [options...] <command> [arguments...]\n\n"
 
             "General options:\n"
-            "   -v         --verbose                  Enable verbose operation\n"
-            "   -T         --local-temp               Use temporary directory inside repository\n"
-            "              --ignore-origin            Don't warn if snapshot not local in update, merge, makepatch\n"
-            "   -z         --compress                 Compress snapshots or patches\n"
-            "   -p         --progress                 Show progress\n\n"
+            "   -v         --verbose                       Enable verbose operation\n"
+            "   -T         --local-temp                    Use temporary directory inside repository\n"
+            "              --ignore-origin                 Don't warn if snapshot not local in update, merge, makepatch\n"
+            "   -z         --compress                      Compress snapshots or patches\n"
+            "   -p         --progress                      Show progress\n\n"
 
             "General commands:\n"
-            "   -h         --help                     Print help and exit\n"
-            "   -V         --version                  Print version and exit\n\n"
+            "   -h         --help                           Print help and exit\n"
+            "   -V         --version                        Print version and exit\n\n"
 
             "Specific commands:\n"
-            "              --list                     List a repository snapshot\n"
-            "                --show-deleted           Show deleted entries of repository snapshot\n"
-            "                --show-by-md             Show files by message digests\n"
-            "                --show-times             Show first and last seen times\n\n"
+            "              --list SNAPSHOT                  List a repository snapshot\n"
+            "                --show-deleted                   Show deleted entries of repository snapshot\n"
+            "                --show-by-md                     Show files by message digests\n"
+            "                --show-times                     Show first and last seen times\n"
+            "                --sort                           Sort chronologically\n\n"
 
-            "              --info                     Show information about a repository or snapshot\n\n"
+            "              --info SNAPSHOT                  Show information about a repository or snapshot\n\n"
 
-            "              --history                  Show history of a repository or snapshot\n\n"
+            "              --history SNAPSHOT               Show history of a repository or snapshot\n\n"
             
-            "              --dump                     Show a structure dump of a repository or snapshot\n\n"
+            "              --dump SNAPSHOT                  Show a structure dump of a repository or snapshot\n\n"
             
-            "              --update                   Update a repository snapshot\n"
-            "     -SSTRING   --snapshot=STRING          Use the specified snapshot file instead of the one contained in the repository\n"
-            "     -CSTRING   --cache=STRING             Use the specified cache file instead of the one contained in the repository\n"
-            "                --no-cache                 Don't use a message digest cache\n"
-            "                --no-purge                 Don't purge obsolete entries from cache after update run\n"
-            "                --ro-cache                 Use read only cache\n\n"
+            "              --update DIRECTORY               Update (or create) a repository snapshot\n"
+            "     -SSTRING   --snapshot=STRING                Use the specified snapshot file instead of the one contained in the repository\n"
+            "     -CSTRING   --cache=STRING                   Use the specified cache file instead of the one contained in the repository\n"
+            "                --no-cache                       Don't use a message digest cache\n"
+            "                --no-purge                       Don't purge obsolete entries from cache after update run\n"
+            "                --ro-cache                       Use read only cache\n\n"
             
-            "              --diff                     Show difference between two repositories or snapshots\n\n"
+            "              --diff SNAPSHOT SNAPSHOT         Show difference between two repositories or snapshots\n\n"
             
-            "              --merge                    Merge a snapshot or a patch into a repository\n"
-            "     -q         --question                 Ask a question before each action\n"
-            "                --prune-empty              Prune empty directories\n"
-            "                --keep-trash               Don't empty trash\n\n"
+            "              --merge SNAPSHOT DIRECTORY       Merge a snapshot into a repository (perform deletes, renames only)\n"
+            "              --merge PATCH DIRECTORY          Merge a patch into a repository\n"
+            "              --merge DIRECTORY DIRECTORY      Merge a repository into a repository\n"
+            "     -q         --question                       Ask a question before each action\n"
+            "     -P         --prune-empty                    Prune empty directories\n"
+            "                --keep-trash                     Don't empty trash\n"
+            "                --check-md                       Check message digest of files prior to deletion or replacement\n"
+            "                --always-copy                    Always copy instead of hard link\n\n"
             
-            "              --makepatch                Make a patch against the specified repository\n"
-            "     -oSTRING   --output-file=STRING       Write output to specified file instead of STDOUT\n"
-            "                --include-all              Include files in patch which do exist on the other side under a different name\n\n"
+            "              --makepatch DIRECTORY SNAPSHOT   Make a patch against the specified repository\n"
+            "     -oSTRING   --output-file=STRING             Write output to specified file instead of STDOUT\n"
+            "                --include-all                    Include files in patch which do exist on the other side under a different name\n\n"
             
-            "              --extract                  Extract the contents of a snapshot or patch\n"
-            "     -DSTRING   --output-directory=STRING  Write output to specified directory\n\n"
+            "              --extract SNAPSHOT               Extract the contents of a snapshot or patch\n"
+            "     -DSTRING   --output-directory=STRING        Write output to specified directory\n\n"
             
-            "              --cleanup                  Remove syrep info from repository\n"
-            "     -lINT      --cleanup-level=INT        1 - just remove temporary data and trash (default)\n"
-            "                                           2 - remove MD cache as well\n"
-            "                                           3 - remove all syrep data\n",
+            "              --cleanup DIRECTORY              Remove syrep info from repository\n"
+            "     -lINT      --cleanup-level=INT              1 - just remove temporary data and trash (default)\n"
+            "                                                 2 - remove MD cache as well\n"
+            "                                                 3 - remove all syrep data\n",
             argv0, argv0);
 
     return 0;
diff --git a/src/syrep.ggo b/src/syrep.ggo
index fea530c..5156944 100644
--- a/src/syrep.ggo
+++ b/src/syrep.ggo
@@ -29,6 +29,7 @@ option "list" - "List a repository snapshot" flag off
  option "show-deleted" - "list: Show deleted entries of repository snapshot" flag off
  option "show-by-md" - "list: Show files by message digests" flag off
  option "show-times" - "list: Show first and last seen times" flag off
+ option "sort" - "list: sort chronologically" flag off
 
 option "info" - "Show information about a repository or snapshot" flag off
 option "history" - "Show history of a repository or snapshot" flag off
@@ -46,8 +47,10 @@ option "diff" - "Show difference between two repositories or snapshots" flag off
 
 option "merge" - "Merge a snapshot or a repository into a repository" flag off
  option "question" q "merge: Ask a question before each action" flag off
- option "prune-empty" - "merge: Prune empty directories" flag off
+ option "prune-empty" P "merge: Prune empty directories" flag off
  option "keep-trash" - "merge: Don't empty trash" flag off
+ option "check-md" - "merge: Check message digest of file before deleting or replacing" flag off
+ option "always-copy" - "merge: Always copy instead of hard linking" flag off
 
 option "makepatch" - "Make a patch against the specified repository" flag off
  option "output-file" o "makepatch: Write output to specified file instead of STDOUT" string no
diff --git a/src/update.c b/src/update.c
index 06986f9..6fc2d06 100644
--- a/src/update.c
+++ b/src/update.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <dirent.h>
 #include <sys/stat.h>
 #include <string.h>
@@ -104,7 +108,8 @@ static int handle_file(struct syrep_db_context *c, uint32_t version, const char
     struct syrep_nrecno nrecno;
 
     memset(&name, 0, sizeof(name));
-    strncpy(name.path, path, PATH_MAX);
+    strncpy(name.path, path, PATH_MAX-1);
+    name.path[PATH_MAX-1] = 0;
 
     if ((r = get_nrecno_by_name(c, &name, &nrecno, 0)) < 0)
         return -1;
diff --git a/src/util.c b/src/util.c
index ffc5dc3..5361e70 100644
--- a/src/util.c
+++ b/src/util.c
@@ -18,6 +18,10 @@
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ***/
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdio.h>
 #include <assert.h>
 #include <stdlib.h>
@@ -499,11 +503,11 @@ int prune_empty_directories(const char *path, const char *root) {
     char rroot[PATH_MAX],
          rpath[PATH_MAX];
 
-    strncpy(rroot, root, PATH_MAX);
+    strncpy(rroot, root, PATH_MAX-1);
     rroot[PATH_MAX-1] = 0;
     normalize_path(rroot);
 
-    strncpy(rpath, path, PATH_MAX);
+    strncpy(rpath, path, PATH_MAX-1);
     rpath[PATH_MAX-1] = 0;
     normalize_path(rpath);
 
@@ -545,7 +549,7 @@ int mkdir_p(const char *path, mode_t m) {
     char *e, *b;
     int quit = 0;
 
-    strncpy(tmp, path, PATH_MAX);
+    strncpy(tmp, path, PATH_MAX-1);
     tmp[PATH_MAX-1] = 0;
 
     normalize_path(tmp);
@@ -582,7 +586,7 @@ int mkdir_p(const char *path, mode_t m) {
 int makeprefixpath(const char *path, mode_t m) {
     char tmp[PATH_MAX], *e;
 
-    strncpy(tmp, path, PATH_MAX);
+    strncpy(tmp, path, PATH_MAX-1);
     tmp[PATH_MAX-1] = 0;
 
     normalize_path(tmp);