This is a hack that I put together to pull PCAP from multiple instances of stenographer, each with a different configuration file. It adds `mergecap` as a dependency, which is used to produce the final PCAP, which is then filtered through `tcpdump` as before.

stenographer.service

# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# stenographer - full packet to disk capture
#
# stenographer is a simple, fast method of writing live packets to disk,
# then requesting those packets after-the-fact for post-hoc analysis.
[Unit]
Description=packet capture to disk
After=syslog.target network.target

[Service]
Type=oneshot
RemainAfterExit=yes
ExecStart=/bin/true
ExecReload=/bin/true
WorkingDirectory=/etc/stenographer

[Install]
WantedBy=multi-user.target

stenographer@.service

# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# stenographer - full packet to disk capture
#
# stenographer is a simple, fast method of writing live packets to disk,
# then requesting those packets after-the-fact for post-hoc analysis.

[Unit]
Description=packet capture to disk
After=network.target
PartOf=stenographer.service
ReloadPropagatedFrom=stenographer.service

[Service]
User=stenographer
Group=stenographer
SyslogIdentifier=stenographer
LimitFSIZE=4294967296
LimitNOFILE=1000000
ExecStart=/usr/bin/stenographer -config /etc/stenographer/config.%i
ExecStopPost=/bin/pkill -9 stenotype

[Install]
WantedBy=multi-user.target

stenoread

#!/bin/bash
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

if [ "$#" -lt 1 ]; then
  cat >&2 <<EOF
$0 provides a simple method for reading logs out of stenographer.
Its first argument is the query to send to stenographer, all other arguments
are passed to TCPDump.
Examples:
 # Print all packets for source IP 1.1.1.1 without DNS resolution (-n).
 $0 'host 1.1.1.1' -n src host 1.1.1.1
 # Print all PSH packets between 1.1.1.1 and 2.2.2.2:
 $0 'host 1.1.1.1 and host 2.2.2.2' -n 'tcp[tcpflags] & tcp-push != 0'
 # Write all packets between 1.1.1.1 and 2.2.2.2 to disk.
'host 1.1.1.1 and host 2.2.2.2' -w /tmp/out.pcap
See README.md for more details on the Stenographer query language.
Set the STENOGRAPHER_CONFIG environmental variable to point to your stenographer
config if it's in a nonstandard place (defaults to /etc/stenographer/config).
$0 arguments are given before the filter.  These include:
  --limit-bytes X    :  Stop output once we've exceeded X bytes
  --limit-packets X  :  Stop output once we've exceeded X packets
For example:
  # Print first 6 packets or 2K bytes, whichever comes first,
  # from source IP 1.1.1.1
  $0 --limit-packets 6 --limit-bytes 2048 'host 1.1.1.1'
EOF
  exit 1
fi

HEADERS=""
while true; do
  case "$1" in
    --limit-packets)
      HEADERS="$HEADERS --header Steno-Limit-Packets:$2"
      shift 2
      ;;
    --limit-bytes)
      HEADERS="$HEADERS --header Steno-Limit-Bytes:$2"
      shift 2
      ;;
    *)
      STENOQUERY="$1"
      shift
      break
      ;;
  esac
done

TCPDUMP=$(PATH=$PATH:/usr/local/sbin:/usr/sbin:/sbin which tcpdump)
STENOCURL=$(PATH=$(dirname "$0"):$PATH which stenocurl)

STENOGRAPHER_CONFIG_BASE=/etc/stenographer/config.
INTERFACES=$(ls ${STENOGRAPHER_CONFIG_BASE}* | awk -F. '{ print $2 }')
OUT=$(mktemp -d /tmp/stenoread.XXXXXXXXXX) || { echo "Failed to create temp file"; exit 1; }

echo "Running stenographer query '$STENOQUERY', piping to 'tcpdump $@'" >&2

for IFACE in ${INTERFACES[@]}
do
  STENOGRAPHER_CONFIG="${STENOGRAPHER_CONFIG_BASE}${IFACE}"
  "$STENOCURL" /query \
    -d "$STENOQUERY" \
    --silent \
    --max-time 890 \
    --show-error $HEADERS |
    "$TCPDUMP" -r /dev/stdin -s 0 -w ${OUT}/${IFACE}.pcap  &>/dev/null
done

mergecap -w - ${OUT}/*.pcap | tcpdump -r /dev/stdin -s 0 "$@"
rm -rf ${OUT}