Index: src/add.c
==================================================================
--- src/add.c
+++ src/add.c
@@ -78,11 +78,11 @@
   static int numManifests;
 
   if( cachedManifest == -1 ){
     int i;
     Blob repo;
-    cachedManifest = db_get_manifest_setting();
+    cachedManifest = db_get_manifest_setting(0);
     numManifests = 0;
     for(i=0; i<count(aManifestflags); i++){
       if( cachedManifest&aManifestflags[i].flg ) {
         azManifests[numManifests++] = aManifestflags[i].fname;
       }

Index: src/checkin.c
==================================================================
--- src/checkin.c
+++ src/checkin.c
@@ -2553,11 +2553,11 @@
   sCiInfo.zUserOvrd = find_option("user-override",0,1);
   noSign = db_get_boolean("omitsign", 0)|noSign;
   if( db_get_boolean("clearsign", 0)==0 ){ noSign = 1; }
   useCksum = db_get_boolean("repo-cksum", 1);
   bIgnoreSkew = find_option("ignore-clock-skew",0,0)!=0;
-  outputManifest = db_get_manifest_setting();
+  outputManifest = db_get_manifest_setting(0);
   mxSize = db_large_file_size();
   if( find_option("ignore-oversize",0,0)!=0 ) mxSize = 0;
   verify_all_options();
 
   /* Get the ID of the parent manifest artifact */

Index: src/checkout.c
==================================================================
--- src/checkout.c
+++ src/checkout.c
@@ -173,11 +173,11 @@
 */
 void manifest_to_disk(int vid){
   char *zManFile;
   int flg;
 
-  flg = db_get_manifest_setting();
+  flg = db_get_manifest_setting(0);
 
   if( flg & MFESTFLG_RAW ){
     Blob manifest = BLOB_INITIALIZER;
     content_get(vid, &manifest);
     sterilize_manifest(&manifest, CFTYPE_MANIFEST);

Index: src/db.c
==================================================================
--- src/db.c
+++ src/db.c
@@ -3647,66 +3647,79 @@
 **
 ** If the zNonVersionedSetting parameter is not NULL then it holds the
 ** non-versioned value for this setting.  If both a versioned and a
 ** non-versioned value exist and are not equal, then a warning message
 ** might be generated.
+**
+** zCkin is normally NULL.  In that case, the versioned setting is
+** take from the local check-out, if a local checkout exists, or from
+** checkin named by the g.zOpenRevision global variable.  If zCkin is
+** not NULL, then zCkin is the name of the specific checkin from which
+** versioned setting value is taken.  When zCkin is not NULL, the cache
+** is bypassed.
 */
-char *db_get_versioned(const char *zName, char *zNonVersionedSetting){
+char *db_get_versioned(
+  const char *zName,
+  char *zNonVersionedSetting,
+  const char *zCkin
+){
   char *zVersionedSetting = 0;
   int noWarn = 0;
   int found = 0;
   struct _cacheEntry {
     struct _cacheEntry *next;
     const char *zName, *zValue;
   } *cacheEntry = 0;
   static struct _cacheEntry *cache = 0;
 
-  if( !g.localOpen && g.zOpenRevision==0 ) return zNonVersionedSetting;
+  if( !g.localOpen && g.zOpenRevision==0 && zCkin==0 ){
+    return zNonVersionedSetting;
+  }
+
   /* Look up name in cache */
-  cacheEntry = cache;
-  while( cacheEntry!=0 ){
-    if( fossil_strcmp(cacheEntry->zName, zName)==0 ){
-      zVersionedSetting = fossil_strdup(cacheEntry->zValue);
-      break;
-    }
-    cacheEntry = cacheEntry->next;
-  }
+  if( zCkin==0 ){
+    cacheEntry = cache;
+    while( cacheEntry!=0 ){
+      if( fossil_strcmp(cacheEntry->zName, zName)==0 ){
+        zVersionedSetting = fossil_strdup(cacheEntry->zValue);
+        break;
+      }
+      cacheEntry = cacheEntry->next;
+    }
+  }
+
   /* Attempt to read value from file in check-out if there wasn't a cache hit.*/
   if( cacheEntry==0 ){
     Blob versionedPathname;
     Blob setting;
-    blob_zero(&versionedPathname);
-    blob_zero(&setting);
-    blob_appendf(&versionedPathname, "%s.fossil-settings/%s",
-                 g.zLocalRoot, zName);
-    if( !g.localOpen ){
-      /* Repository is in the process of being opened, but files have not been
-       * written to disk. Load from the database. */
-      Blob noWarnFile;
-      if( historical_blob(g.zOpenRevision, blob_str(&versionedPathname),
-          &setting, 0) ){
-        found = 1;
-      }
-      /* See if there's a no-warn flag */
-      blob_append(&versionedPathname, ".no-warn", -1);
-      blob_zero(&noWarnFile);
-      if( historical_blob(g.zOpenRevision, blob_str(&versionedPathname),
-          &noWarnFile, 0) ){
-        noWarn = 1;
-      }
-      blob_reset(&noWarnFile);
-    }else if( file_size(blob_str(&versionedPathname), ExtFILE)>=0 ){
-      /* File exists, and contains the value for this setting. Load from
-      ** the file. */
-      const char *zFile = blob_str(&versionedPathname);
-      if( blob_read_from_file(&setting, zFile, ExtFILE)>=0 ){
-        found = 1;
-      }
-      /* See if there's a no-warn flag */
-      blob_append(&versionedPathname, ".no-warn", -1);
-      if( file_size(blob_str(&versionedPathname), ExtFILE)>=0 ){
-        noWarn = 1;
+    blob_init(&versionedPathname, 0, 0);
+    blob_init(&setting, 0, 0);
+    if( !g.localOpen || zCkin!=0 ){
+      /* Repository is in the process of being opened, but files have not been
+       * written to disk. Load from the database. */
+      blob_appendf(&versionedPathname, ".fossil-settings/%s", zName);
+      if( historical_blob(zCkin ? zCkin : g.zOpenRevision,
+                          blob_str(&versionedPathname),
+                          &setting, 0)
+      ){
+        found = 1;
+      }
+    }else{
+      blob_appendf(&versionedPathname, "%s.fossil-settings/%s",
+                   g.zLocalRoot, zName);
+      if( file_size(blob_str(&versionedPathname), ExtFILE)>=0 ){
+        /* File exists, and contains the value for this setting. Load from
+        ** the file. */
+        const char *zFile = blob_str(&versionedPathname);
+        if( blob_read_from_file(&setting, zFile, ExtFILE)>=0 ){
+          found = 1;
+        }
+        /* See if there's a no-warn flag */
+        blob_append(&versionedPathname, ".no-warn", -1);
+        if( file_size(blob_str(&versionedPathname), ExtFILE)>=0 ){
+          noWarn = 1;
+        }
       }
     }
     blob_reset(&versionedPathname);
     if( found ){
       blob_strip_comment_lines(&setting, &setting);
@@ -3713,20 +3726,27 @@
       blob_trim(&setting); /* Avoid non-obvious problems with line endings
                            ** on boolean properties */
       zVersionedSetting = fossil_strdup(blob_str(&setting));
     }
     blob_reset(&setting);
+
     /* Store result in cache, which can be the value or 0 if not found */
-    cacheEntry = (struct _cacheEntry*)fossil_malloc(sizeof(struct _cacheEntry));
-    cacheEntry->next = cache;
-    cacheEntry->zName = zName;
-    cacheEntry->zValue = fossil_strdup(zVersionedSetting);
-    cache = cacheEntry;
+    if( zCkin==0 ){
+      cacheEntry = (struct _cacheEntry*)fossil_malloc(sizeof(*cacheEntry));
+      cacheEntry->next = cache;
+      cacheEntry->zName = zName;
+      cacheEntry->zValue = fossil_strdup(zVersionedSetting);
+      cache = cacheEntry;
+    }
   }
+
   /* Display a warning? */
-  if( zVersionedSetting!=0 && zNonVersionedSetting!=0
-   && zNonVersionedSetting[0]!='\0' && !noWarn
+  if( zVersionedSetting!=0
+   && zNonVersionedSetting!=0
+   && zNonVersionedSetting[0]!='\0'
+   && zCkin==0
+   && !noWarn
   ){
     /* There's a versioned setting, and a non-versioned setting. Tell
     ** the user about the conflict */
     fossil_warning(
         "setting %s has both versioned and non-versioned values: using "
@@ -3735,10 +3755,11 @@
         "\"%/.fossil-settings/%s.no-warn\" in the check-out root, or delete "
         "the non-versioned setting with \"fossil unset %s\")", zName,
         g.zLocalRoot, zName, g.zLocalRoot, zName, zName
     );
   }
+
   /* Prefer the versioned setting */
   return ( zVersionedSetting!=0 ) ? zVersionedSetting : zNonVersionedSetting;
 }
 
 
@@ -3778,11 +3799,11 @@
   }
   if( pSetting!=0 && pSetting->versionable ){
     /* This is a versionable setting, try and get the info from a
     ** checked-out file */
     char * zZ = z;
-    z = db_get_versioned(zName, z);
+    z = db_get_versioned(zName, z, 0);
     if(zZ != z){
       fossil_free(zZ);
     }
   }
   if( z==0 ){
@@ -3919,11 +3940,11 @@
   }
   fossil_free(zVal);
   return dflt;
 }
 int db_get_versioned_boolean(const char *zName, int dflt){
-  char *zVal = db_get_versioned(zName, 0);
+  char *zVal = db_get_versioned(zName, 0, 0);
   if( zVal==0 ) return dflt;
   if( is_truth(zVal) ) return 1;
   if( is_false(zVal) ) return 0;
   return dflt;
 }
@@ -4048,14 +4069,30 @@
 ** Get the manifest setting.  For backwards compatibility first check if the
 ** value is a boolean.  If it's not a boolean, treat each character as a flag
 ** to enable a manifest type.  This system puts certain boundary conditions on
 ** which letters can be used to represent flags (any permutation of flags must
 ** not be able to fully form one of the boolean values).
+**
+** "manifest" is a versionable setting.  But we do not issue a warning
+** if there is a conflict.  Instead, the value returned is the value for
+** the versioned setting if the versioned setting exists, or the ordinary
+** setting otherwise.
+**
+** The argument zCkin is the specific check-in for which we want the
+** manifest setting.
 */
-int db_get_manifest_setting(void){
+int db_get_manifest_setting(const char *zCkin){
   int flg;
-  char *zVal = db_get("manifest", 0);
+  char *zVal;
+  
+  /* Look for the versioned setting first */
+  zVal = db_get_versioned("manifest", 0, zCkin);
+
+  if( zVal==0 && g.repositoryOpen ){
+    /* No versioned setting, look for the repository setting second */
+    zVal = db_text(0, "SELECT value FROM config WHERE name='manifest'");
+  }
   if( zVal==0 || is_false(zVal) ){
     return 0;
   }else if( is_truth(zVal) ){
     return MFESTFLG_RAW|MFESTFLG_UUID;
   }
@@ -4068,10 +4105,37 @@
     }
     zVal++;
   }
   return flg;
 }
+
+/*
+** COMMAND: test-manifest-setting
+**
+** Usage: %fossil test-manifest-setting VERSION VERSION ...
+**
+** Display the value for the "manifest" setting for various versions
+** of the repository.
+*/
+void test_manfest_setting_cmd(void){
+  int i;
+  db_find_and_open_repository(0, 0);
+  for(i=2; i<g.argc; i++){
+    int m = db_get_manifest_setting(g.argv[i]);
+    fossil_print("%s:\n", g.argv[i]);
+    fossil_print("   flags = 0x%02x\n", m);
+    if( m & MFESTFLG_RAW ){
+      fossil_print("   manifest\n");
+    }
+    if( m & MFESTFLG_UUID ){
+      fossil_print("   manifest.uuid\n");
+    }
+    if( m & MFESTFLG_TAGS ){
+      fossil_print("   manifest.tags\n");
+    }
+  }
+}
 
 
 /*
 ** Record the name of a local repository in the global_config() database.
 ** The repository filename %s is recorded as an entry with a "name" field
@@ -4391,11 +4455,11 @@
       versioned = 1;
     }
     blob_reset(&versionedPathname);
   }
   if( valueOnly && versioned ){
-    fossil_print("%s\n", db_get_versioned(pSetting->name, NULL));
+    fossil_print("%s\n", db_get_versioned(pSetting->name, NULL, NULL));
     return;
   }
   if( g.repositoryOpen ){
     db_prepare(&q,
        "SELECT '(local)', value FROM config WHERE name=%Q"

Index: src/export.c
==================================================================
--- src/export.c
+++ src/export.c
@@ -1074,12 +1074,11 @@
 */
 static int gitmirror_send_checkin(
   FILE *xCmd,           /* Write fast-import text on this pipe */
   int rid,              /* BLOB.RID for the check-in to export */
   const char *zUuid,    /* BLOB.UUID for the check-in to export */
-  int *pnLimit,         /* Stop when the counter reaches zero */
-  int fManifest         /* MFESTFLG_* values */
+  int *pnLimit          /* Stop when the counter reaches zero */
 ){
   Manifest *pMan;       /* The check-in to be output */
   int i;                /* Loop counter */
   int iParent;          /* Which immediate ancestor is primary.  -1 for none */
   Stmt q;               /* An SQL query */
@@ -1089,10 +1088,12 @@
   Blob comment;         /* The comment text for the check-in */
   int nErr = 0;         /* Number of errors */
   int bPhantomOk;       /* True if phantom files should be ignored */
   char buf[24];
   char *zEmail;         /* Contact info for Git committer field */
+  int fManifest;        /* Should the manifest files be included? */
+  int fPManifest = 0;   /* OR of the manifest files for all parents */
 
   pMan = manifest_get(rid, CFTYPE_MANIFEST, 0);
   if( pMan==0 ){
     /* Must be a phantom.  Return without doing anything, and in particular
     ** without creating a mark for this check-in. */
@@ -1106,11 +1107,11 @@
     char *zPMark = gitmirror_find_mark(pMan->azParent[i], 0, 0);
     if( zPMark==0 ){
       int prid = db_int(0, "SELECT rid FROM blob WHERE uuid=%Q",
                         pMan->azParent[i]);
       int rc = gitmirror_send_checkin(xCmd, prid, pMan->azParent[i],
-                                      pnLimit, fManifest);
+                                      pnLimit);
       if( rc || *pnLimit<=0 ){
         manifest_destroy(pMan);
         return 1;
       }
     }
@@ -1215,10 +1216,11 @@
   blob_reset(&comment);
   iParent = -1;  /* Which ancestor is the primary parent */
   for(i=0; i<pMan->nParent; i++){
     char *zOther = gitmirror_find_mark(pMan->azParent[i],0,0);
     if( zOther==0 ) continue;
+    fPManifest |= db_get_manifest_setting(pMan->azParent[i]);
     if( iParent<0 ){
       iParent = i;
       fprintf(xCmd, "from %s\n", zOther);
     }else{
       fprintf(xCmd, "merge %s\n", zOther);
@@ -1271,29 +1273,36 @@
   db_finalize(&q);
   manifest_destroy(pMan);
   pMan = 0;
 
   /* Include Fossil-generated auxiliary files in the check-in */
+  fManifest = db_get_manifest_setting(zUuid);
   if( fManifest & MFESTFLG_RAW ){
     Blob manifest;
     content_get(rid, &manifest);
     sterilize_manifest(&manifest, CFTYPE_MANIFEST);
     fprintf(xCmd,"M 100644 inline manifest\ndata %d\n%s\n",
       blob_strlen(&manifest), blob_str(&manifest));
     blob_reset(&manifest);
+  }else if( fPManifest & MFESTFLG_RAW ){
+    fprintf(xCmd, "D manifest\n");
   }
   if( fManifest & MFESTFLG_UUID ){
     int n = (int)strlen(zUuid);
     fprintf(xCmd,"M 100644 inline manifest.uuid\ndata %d\n%s\n\n", n+1, zUuid);
+  }else if( fPManifest & MFESTFLG_UUID ){
+    fprintf(xCmd, "D manifest.uuid\n");
   }
   if( fManifest & MFESTFLG_TAGS ){
     Blob tagslist;
     blob_init(&tagslist, 0, 0);
     get_checkin_taglist(rid, &tagslist);
     fprintf(xCmd,"M 100644 inline manifest.tags\ndata %d\n%s\n",
       blob_strlen(&tagslist), blob_str(&tagslist));
     blob_reset(&tagslist);
+  }else if( fPManifest & MFESTFLG_TAGS ){
+    fprintf(xCmd, "D manifest.tags\n");
   }
 
   /* The check-in is finished, so decrement the counter */
   (*pnLimit)--;
   return 0;
@@ -1383,11 +1392,10 @@
   char *zPushUrl;                 /* URL to sync the mirror to */
   double rEnd;                    /* time of most recent export */
   int rc;                         /* Result code */
   int bForce;                     /* Do the export and sync even if no changes*/
   int bNeedRepack = 0;            /* True if we should run repack at the end */
-  int fManifest;                  /* Current "manifest" setting */
   int bIfExists;                  /* The --if-mirrored flag */
   FILE *xCmd;                     /* Pipe to the "git fast-import" command */
   FILE *pMarks;                   /* Git mark files */
   Stmt q;                         /* Queries */
   char zLine[200];                /* One line of a mark file */
@@ -1521,13 +1529,10 @@
     gitmirror_message(VERB_NORMAL, "no changes\n");
     db_commit_transaction();
     return;
   }
 
-  /* Do we need to include manifest files in the clone? */
-  fManifest = db_get_manifest_setting();
-
   /* Change to the MIRROR directory so that the Git commands will work */
   rc = file_chdir(zMirror, 0);
   if( rc ) fossil_fatal("cannot change the working directory to \"%s\"",
                         zMirror);
 
@@ -1579,11 +1584,11 @@
   while( nLimit && db_step(&q)==SQLITE_ROW ){
     int rid = db_column_int(&q, 0);
     double rMTime = db_column_double(&q, 1);
     const char *zUuid = db_column_text(&q, 2);
     if( rMTime>rEnd ) rEnd = rMTime;
-    rc = gitmirror_send_checkin(xCmd, rid, zUuid, &nLimit, fManifest);
+    rc = gitmirror_send_checkin(xCmd, rid, zUuid, &nLimit);
     if( rc ) break;
     gitmirror_message(VERB_NORMAL,"%d/%d      \r", nTotal-nLimit, nTotal);
     fflush(stdout);
   }
   db_finalize(&q);

Index: src/setup.c
==================================================================
--- src/setup.c
+++ src/setup.c
@@ -1157,11 +1157,11 @@
   @ <table border="0"><tr><td valign="top">
   login_insert_csrf_secret();
   for(i=0, pSet=aSetting; i<nSetting; i++, pSet++){
     if( pSet->width==0 ){
       int hasVersionableValue = pSet->versionable &&
-          (db_get_versioned(pSet->name, NULL)!=0);
+          (db_get_versioned(pSet->name, NULL, NULL)!=0);
       onoff_attribute("", pSet->name,
                       pSet->var!=0 ? pSet->var : pSet->name /*works-like:"x"*/,
                       is_truth(pSet->def), hasVersionableValue);
       @ <a href='%R/help?cmd=%s(pSet->name)'>%h(pSet->name)</a>
       if( pSet->versionable ){
@@ -1175,11 +1175,11 @@
   @ </td><td style="width:50px;"></td><td valign="top">
   @ <table>
   for(i=0, pSet=aSetting; i<nSetting; i++, pSet++){
     if( pSet->width>0 && !pSet->forceTextArea ){
       int hasVersionableValue = pSet->versionable &&
-          (db_get_versioned(pSet->name, NULL)!=0);
+          (db_get_versioned(pSet->name, NULL, NULL)!=0);
       @ <tr><td>
       @ <a href='%R/help?cmd=%s(pSet->name)'>%h(pSet->name)</a>
       if( pSet->versionable ){
         @  (v)
       } else {
@@ -1194,11 +1194,11 @@
   }
   @</table>
   @ </td><td style="width:50px;"></td><td valign="top">
   for(i=0, pSet=aSetting; i<nSetting; i++, pSet++){
     if( pSet->width>0 && pSet->forceTextArea ){
-      int hasVersionableValue = db_get_versioned(pSet->name, NULL)!=0;
+      int hasVersionableValue = db_get_versioned(pSet->name, NULL, NULL)!=0;
       @ <a href='%R/help?cmd=%s(pSet->name)'>%s(pSet->name)</a>
       if( pSet->versionable ){
         @  (v)<br>
       } else {
         @ <br>

Index: src/tar.c
==================================================================
--- src/tar.c
+++ src/tar.c
@@ -499,11 +499,11 @@
   pManifest = manifest_get(rid, CFTYPE_MANIFEST, 0);
   if( pManifest ){
     int flg, eflg = 0;
     mTime = (unsigned)((pManifest->rDate - 2440587.5)*86400.0);
     if( pTar ) tar_begin(mTime);
-    flg = db_get_manifest_setting();
+    flg = db_get_manifest_setting(blob_str(&hash));
     if( flg ){
       /* eflg is the effective flags, taking include/exclude into account */
       if( (pInclude==0 || glob_match(pInclude, "manifest"))
        && !glob_match(pExclude, "manifest")
        && (flg & MFESTFLG_RAW) ){

Index: src/zip.c
==================================================================
--- src/zip.c
+++ src/zip.c
@@ -652,11 +652,11 @@
   pManifest = manifest_get(rid, CFTYPE_MANIFEST, 0);
   if( pManifest ){
     int flg, eflg = 0;
     char *zName = 0;
     zip_set_timedate(pManifest->rDate);
-    flg = db_get_manifest_setting();
+    flg = db_get_manifest_setting(blob_str(&hash));
     if( flg ){
       /* eflg is the effective flags, taking include/exclude into account */
       if( (pInclude==0 || glob_match(pInclude, "manifest"))
        && !glob_match(pExclude, "manifest")
        && (flg & MFESTFLG_RAW) ){