puppet: Match the x bits on directories to what puppet actually does.

Puppet _always_ sets the `+x` bit on directories if they have the `r`
bit set for that slot[^1]:

> When specifying numeric permissions for directories, Puppet sets the
> search permission wherever the read permission is set.

As such, for instance, `0640` is actually applied as `0750`.

Fix what we "want" to match what puppet is applying, by adding the `x`
bit.  In none of these cases did we actually intend the directory to
not be executable.

[1] https://www.puppet.com/docs/puppet/5.5/types/file.html#file-attribute-mode

puppet/zulip_ops/manifests/apache.pp

@@ -19,7 +19,7 @@ class zulip_ops::apache {
     require => Package['apache2'],
     owner   => 'root',
     group   => 'root',
-    mode    => '0644',
+    mode    => '0755',
   }
 
   file { '/etc/apache2/ports.conf':
@@ -37,6 +37,6 @@ class zulip_ops::apache {
     require => Package[apache2],
     owner   => 'root',
     group   => 'root',
-    mode    => '0640',
+    mode    => '0750',
   }
 }

puppet/zulip_ops/manifests/profile/base.pp

@@ -64,7 +64,7 @@ class zulip_ops::profile::base {
     require => User['zulip'],
     owner   => 'zulip',
     group   => 'zulip',
-    mode    => '0600',
+    mode    => '0700',
   }
 
   # Clear /etc/update-motd.d, to fix load problems with Nagios
@@ -170,14 +170,14 @@ class zulip_ops::profile::base {
     require => User['nagios'],
     owner   => 'nagios',
     group   => 'nagios',
-    mode    => '0600',
+    mode    => '0700',
   }
   file { '/var/lib/nagios/.ssh':
     ensure  => directory,
     require => File['/var/lib/nagios/'],
     owner   => 'nagios',
     group   => 'nagios',
-    mode    => '0600',
+    mode    => '0700',
   }
   file { '/home/nagios':
     ensure  => absent,

puppet/zulip_ops/manifests/profile/grafana.pp

@@ -60,7 +60,7 @@ class zulip_ops::profile::grafana {
     ensure => directory,
     owner  => 'root',
     group  => 'root',
-    mode   => '0644',
+    mode   => '0755',
   }
   file { '/etc/grafana/grafana.ini':
     ensure => file,

puppet/zulip_ops/manifests/profile/prometheus_server.pp

@@ -32,7 +32,7 @@ class zulip_ops::profile::prometheus_server {
     ensure => directory,
     owner  => 'root',
     group  => 'root',
-    mode   => '0644',
+    mode   => '0755',
   }
   file { '/etc/prometheus/prometheus.yaml':
     ensure => file,

puppet/zulip_ops/manifests/profile/zmirror_personals.pp

@@ -30,7 +30,7 @@ class zulip_ops::profile::zmirror_personals {
   file { ['/home/zulip/api-keys', '/home/zulip/zephyr_sessions', '/home/zulip/ccache',
           '/home/zulip/mirror_status']:
     ensure => directory,
-    mode   => '0644',
+    mode   => '0755',
     owner  => 'zulip',
     group  => 'zulip',
   }