Here is my previous review comments in a squashable patch form.  The
result seems to pass all 27 combinations (fetch.prune, remote.*.prune
and command line all are tristate yes/no/unspecified).

Without the fix-up in *.c files, three combinations seem to fail.

 Documentation/config.txt |   3 +-
 builtin/fetch.c          |  41 +++++++++-------
 remote.c                 |   1 +
 t/t5510-fetch.sh         | 118 ++++++++++++++++++++++++++++++++---------------
 4 files changed, 108 insertions(+), 55 deletions(-)

diff --git a/Documentation/config.txt b/Documentation/config.txt
index fc39f3a..e4ce7c4 100644
--- a/Documentation/config.txt
+++ b/Documentation/config.txt
@@ -1051,7 +1051,7 @@ fetch.unpackLimit::
 
 fetch.prune::
        If true, fetch will automatically behave as if the `--prune`
-       option was given on the command line.
+       option was given on the command line.  See also `remote.<name>.prune`.
 
 format.attach::
        Enable multipart/mixed attachments as the default for
@@ -1992,6 +1992,7 @@ remote.<name>.prune::
        When set to true, fetching from this remote by default will also
        remove any remote-tracking branches which no longer exist on the
        remote (as if the `--prune` option was give on the command line).
+       Overrides `fetch.prune` settings, if any.
 
 remotes.<group>::
        The list of remotes which are fetched by "git remote update
diff --git a/builtin/fetch.c b/builtin/fetch.c
index 082450b..08ab948 100644
--- a/builtin/fetch.c
+++ b/builtin/fetch.c
@@ -30,13 +30,10 @@ enum {
        TAGS_SET = 2
 };
 
-enum {
-       PRUNE_UNSET = 0,
-       PRUNE_DEFAULT = 1,
-       PRUNE_FORCE = 2
-};
+static int fetch_prune_config = -1; /* unspecified */
+static int prune = -1; /* unspecified */
+#define PRUNE_BY_DEFAULT 0 /* do we prune by default? */
 
-static int prune = PRUNE_DEFAULT;
 static int all, append, dry_run, force, keep, multiple, update_head_ok, 
verbosity;
 static int progress = -1, recurse_submodules = RECURSE_SUBMODULES_DEFAULT;
 static int tags = TAGS_DEFAULT, unshallow;
@@ -64,12 +61,10 @@ static int option_parse_recurse_submodules(const struct 
option *opt,
 static int git_fetch_config(const char *k, const char *v, void *cb)
 {
        if (!strcmp(k, "fetch.prune")) {
-               int boolval = git_config_bool(k, v);
-               if (boolval)
-                       prune = PRUNE_FORCE;
+               fetch_prune_config = git_config_bool(k, v);
                return 0;
        }
-       return git_default_config(k, v, cb);
+       return 0;
 }
 
 static struct option builtin_fetch_options[] = {
@@ -87,8 +82,8 @@ static struct option builtin_fetch_options[] = {
                    N_("fetch all tags and associated objects"), TAGS_SET),
        OPT_SET_INT('n', NULL, &tags,
                    N_("do not fetch all tags (--no-tags)"), TAGS_UNSET),
-       OPT_BOOLEAN('p', "prune", &prune,
-                   N_("prune remote-tracking branches no longer on remote")),
+       OPT_BOOL('p', "prune", &prune,
+                N_("prune remote-tracking branches no longer on remote")),
        { OPTION_CALLBACK, 0, "recurse-submodules", NULL, N_("on-demand"),
                    N_("control recursive fetching of submodules"),
                    PARSE_OPT_OPTARG, option_parse_recurse_submodules },
@@ -756,8 +751,11 @@ static int do_fetch(struct transport *transport,
                free_refs(ref_map);
                return 1;
        }
-       if (prune == PRUNE_FORCE || (transport->remote->prune && prune)) {
-               /* If --tags was specified, pretend the user gave us the 
canonical tags refspec */
+       if (prune) {
+               /*
+                * If --tags was specified, pretend that the user gave us
+                * the canonical tags refspec
+                */
                if (tags == TAGS_SET) {
                        const char *tags_str = "refs/tags/*:refs/tags/*";
                        struct refspec *tags_refspec, *refspec;
@@ -866,10 +864,8 @@ static void add_options_to_argv(struct argv_array *argv)
 {
        if (dry_run)
                argv_array_push(argv, "--dry-run");
-       if (prune == PRUNE_FORCE)
+       if (prune > 0)
                argv_array_push(argv, "--prune");
-       else if (prune == PRUNE_UNSET)
-               argv_array_push(argv, "--no-prune");
        if (update_head_ok)
                argv_array_push(argv, "--update-head-ok");
        if (force)
@@ -936,6 +932,17 @@ static int fetch_one(struct remote *remote, int argc, 
const char **argv)
                    "remote name from which new revisions should be fetched."));
 
        transport = transport_get(remote, NULL);
+
+       if (prune < 0) {
+               /* no command line request */
+               if (0 <= transport->remote->prune)
+                       prune = transport->remote->prune;
+               else if (0 <= fetch_prune_config)
+                       prune = fetch_prune_config;
+               else
+                       prune = PRUNE_BY_DEFAULT;
+       }
+
        transport_set_verbosity(transport, verbosity, progress);
        if (upload_pack)
                set_option(TRANS_OPT_UPLOADPACK, upload_pack);
diff --git a/remote.c b/remote.c
index d0ddbef..89be211 100644
--- a/remote.c
+++ b/remote.c
@@ -148,6 +148,7 @@ static struct remote *make_remote(const char *name, int len)
        }
 
        ret = xcalloc(1, sizeof(struct remote));
+       ret->prune = -1;  /* unspecified */
        ALLOC_GROW(remotes, remotes_nr + 1, remotes_alloc);
        remotes[remotes_nr++] = ret;
        if (len)
diff --git a/t/t5510-fetch.sh b/t/t5510-fetch.sh
index 33fe3d5..019535f 100755
--- a/t/t5510-fetch.sh
+++ b/t/t5510-fetch.sh
@@ -471,43 +471,87 @@ test_expect_success "should be able to fetch with 
duplicate refspecs" '
        )
 '
 
-test_expect_success 'fetch should prune when fetch.prune is true' '
-  cd "$D" &&
-  git branch somebranch &&
-  (
-    cd one &&
-    git fetch &&
-    test -f .git/refs/remotes/origin/somebranch
-  ) &&
-  git branch -d somebranch &&
-  (
-    cd one &&
-    git config fetch.prune true &&
-    git fetch --no-prune &&
-    test -f .git/refs/remotes/origin/somebranch &&
-    git fetch &&
-    ! test -f .git/refs/remotes/origin/somebranch
-  )
-'
-
-test_expect_success 'fetch should prune when remote.<name>.prune is true' '
-  cd "$D" &&
-  git branch somebranch &&
-  (
-    cd one &&
-    git fetch &&
-    test -f .git/refs/remotes/origin/somebranch
-  ) &&
-  git branch -d somebranch &&
-  (
-    cd one &&
-    git config remote.origin.prune true &&
-    git fetch --no-prune &&
-    test -f .git/refs/remotes/origin/somebranch &&
-    git fetch &&
-    ! test -f .git/refs/remotes/origin/somebranch
-  )
-'
+# configured prune tests
+
+set_config_tristate () {
+       # var=$1 val=$2
+       case "$2" in
+       unset)  test_unconfig "$1" ;;
+       *)      git config "$1" "$2" ;;
+       esac
+}
+
+test_configured_prune () {
+       fetch_prune=$1 remote_origin_prune=$2 cmdline=$3 expected=$4
+
+       test_expect_success "prune fetch.prune=$1 remote.origin.prune=$2${3:+ 
$3}; $4" '
+               # make sure a newbranch is there in . and also in one
+               git branch -f newbranch &&
+               (
+                       cd one &&
+                       test_unconfig fetch.prune &&
+                       test_unconfig remote.origin.prune &&
+                       git fetch &&
+                       git rev-parse --verify refs/remotes/origin/newbranch
+               )
+
+               # now remove it
+               git branch -d newbranch &&
+
+               # then test
+               (
+                       cd one &&
+                       set_config_tristate fetch.prune $fetch_prune &&
+                       set_config_tristate remote.origin.prune 
$remote_origin_prune &&
+
+                       git fetch $cmdline &&
+                       case "$expected" in
+                       pruned)
+                               test_must_fail git rev-parse --verify 
refs/remotes/origin/newbranch
+                               ;;
+                       kept)
+                               git rev-parse --verify 
refs/remotes/origin/newbranch
+                               ;;
+                       esac
+               )
+       '
+}
+
+test_configured_prune unset unset ""           kept
+test_configured_prune unset unset "--no-prune" kept
+test_configured_prune unset unset "--prune"    pruned
+
+test_configured_prune false unset ""           kept
+test_configured_prune false unset "--no-prune" kept
+test_configured_prune false unset "--prune"    pruned
+
+test_configured_prune true  unset ""           pruned
+test_configured_prune true  unset "--prune"    pruned
+test_configured_prune true  unset "--no-prune" kept
+
+test_configured_prune unset false ""           kept
+test_configured_prune unset false "--no-prune" kept
+test_configured_prune unset false "--prune"    pruned
+
+test_configured_prune false false ""           kept
+test_configured_prune false false "--no-prune" kept
+test_configured_prune false false "--prune"    pruned
+
+test_configured_prune true  false ""           kept
+test_configured_prune true  false "--prune"    pruned
+test_configured_prune true  false "--no-prune" kept
+
+test_configured_prune unset true  ""           pruned
+test_configured_prune unset true  "--no-prune" kept
+test_configured_prune unset true  "--prune"    pruned
+
+test_configured_prune false true  ""           pruned
+test_configured_prune false true  "--no-prune" kept
+test_configured_prune false true  "--prune"    pruned
+
+test_configured_prune true  true  ""           pruned
+test_configured_prune true  true  "--prune"    pruned
+test_configured_prune true  true  "--no-prune" kept
 
 test_expect_success 'all boundary commits are excluded' '
        test_commit base &&
-- 
1.8.3.2-941-gda9c3c8

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