diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..a125f80
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,7 @@
+**/node_modules
+.eslintrc.json
+.gitignore
+.npmignore
+cloud-config.yaml
+Dockerfile
+run-dev-container
\ No newline at end of file
diff --git a/.npmignore b/.npmignore
new file mode 100644
index 0000000..8ced7ba
--- /dev/null
+++ b/.npmignore
@@ -0,0 +1,6 @@
+.dockerignore
+.eslintrc.json
+.gitignore
+cloud-config.yaml
+Dockerfile
+run-dev-container
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index fc0b398..7f3e924 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,6 @@
 FROM ubuntu:16.04
 
+
 # initialize .ssh directory
 RUN mkdir -p ~/.ssh \
     && chmod 700 ~/.ssh \
@@ -23,9 +24,6 @@ RUN export DEBIAN_FRONTEND=noninteractive \
         mysql-client \
         mysql-server \
         nginx \
-        nodejs \
-        nodejs-legacy \
-        npm \
         openssh-server \
         postfix \
         python \
@@ -38,8 +36,12 @@ RUN export DEBIAN_FRONTEND=noninteractive \
         tmux \
         vim \
     && add-apt-repository -y ppa:ondrej/php \
-    && apt-get update \
+    && add-apt-repository ppa:certbot/certbot \
+    && curl -sL https://deb.nodesource.com/setup_10.x | bash \
+    # && apt-get update \ # above calls apt-get update
     && apt-get install -y --allow-unauthenticated --no-install-recommends \
+        certbot python3-pyasn1 \
+        nodejs \
         php-apcu \
         php5.6-cli \
         php5.6-curl \
@@ -66,14 +68,19 @@ RUN service nginx stop \
 
 
 # install Habitat client and packages for emergence
-RUN curl -s https://raw.githubusercontent.com/habitat-sh/habitat/master/components/hab/install.sh | sudo bash
-RUN hab pkg install jarvus/sencha-cmd/5.1.3.61/20170606195324 jarvus/underscore \
+RUN curl -s https://raw.githubusercontent.com/habitat-sh/habitat/master/components/hab/install.sh | bash
+RUN hab pkg install jarvus/sencha-cmd/6.5.2.15 jarvus/underscore \
     && hab pkg binlink jarvus/sencha-cmd sencha \
     && hab pkg binlink jarvus/underscore underscore
 
 
+# install helpful administrative commands
+RUN npm install -g htpasswd
+
+
 # install emergence
-RUN npm install -g emergence
+COPY . /src
+RUN npm install -g /src
 
 
 # setup and expose emergence
diff --git a/bin/certbot-auth b/bin/certbot-auth
new file mode 100755
index 0000000..40f7b6e
--- /dev/null
+++ b/bin/certbot-auth
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+log () {
+    echo "emergence-certbot-auth: $@"
+}
+
+die () {
+    echo >&2 "emergence-certbot-auth: $@"
+    exit 1
+}
+
+
+# check usage
+[ -n "${CERTBOT_DOMAIN}" ] || die "required environment variable missing: \$CERTBOT_DOMAIN"
+[ -n "${CERTBOT_VALIDATION}" ] || die "required environment variable missing: \$CERTBOT_VALIDATION"
+[ -n "${CERTBOT_TOKEN}" ] || die "required environment variable missing: \$CERTBOT_TOKEN"
+
+
+# determine location of this script
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+
+# resolve site handle for domain
+SITE_HANDLE="$(${DIR}/resolve-site ${CERTBOT_DOMAIN})"
+[ -n "${SITE_HANDLE}" ] || die "could not resolve domain '${CERTBOT_DOMAIN}' under /emergence/sites/*/site.json"
+
+
+# write auth file
+log "writing ${SITE_HANDLE}/${CERTBOT_TOKEN}"
+echo "${CERTBOT_VALIDATION}" | "${DIR}/write-file" "${SITE_HANDLE}" "site-root/.well-known/acme-challenge/${CERTBOT_TOKEN}" || die "failed to write token to VFS"
diff --git a/bin/certbot-cleanup b/bin/certbot-cleanup
new file mode 100755
index 0000000..8984a7e
--- /dev/null
+++ b/bin/certbot-cleanup
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+log () {
+    echo "emergence-certbot-cleanup: $@"
+}
+
+die () {
+    echo >&2 "emergence-certbot-cleanup: $@"
+    exit 1
+}
+
+
+# check usage
+[ -n "${CERTBOT_DOMAIN}" ] || die "required environment variable missing: \$CERTBOT_DOMAIN"
+[ -n "${CERTBOT_TOKEN}" ] || die "required environment variable missing: \$CERTBOT_TOKEN"
+
+
+# determine location of this script
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+
+# resolve site handle for domain
+SITE_HANDLE="$(${DIR}/resolve-site ${CERTBOT_DOMAIN})"
+[ -n "${SITE_HANDLE}" ] || die "could not resolve domain '${CERTBOT_DOMAIN}' under /emergence/sites/*/site.json"
+
+
+# delete auth file
+log "deleting ${SITE_HANDLE}/${CERTBOT_TOKEN}"
+"${DIR}/delete-file" "${SITE_HANDLE}" "site-root/.well-known/acme-challenge/${CERTBOT_TOKEN}" || die "failed to delete token from VFS"
diff --git a/bin/delete-file b/bin/delete-file
new file mode 100755
index 0000000..3765ee0
--- /dev/null
+++ b/bin/delete-file
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+die () {
+    echo >&2 "$@"
+    exit 1
+}
+
+
+# check usage
+[ -n "$1" ] && [ -n "$2" ] || die "Usage: emergence-delete-file <site-handle> <site-file-path>"
+
+
+# determine location of this script
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+
+# execute php script
+cat <<'END_OF_PHP' | "${DIR}/shell" "$1" --stdin "$2"
+<?php
+
+$node = Site::resolvePath($argv[1]);
+
+if (!$node) {
+    error_log('emergence-delete-file: cannot remove \''.$argv[1].'\': No such file');
+    exit(1);
+}
+
+try {
+    $node->delete();
+    exit(0);
+} catch (Exception $e) {
+    error_log('emergence-delete-file: failed to delete file from VFS: '.$e->getMessage());
+    exit(1);
+}
+
+END_OF_PHP
+
+
diff --git a/bin/read-file b/bin/read-file
new file mode 100755
index 0000000..76c8b25
--- /dev/null
+++ b/bin/read-file
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+die () {
+    echo >&2 "$@"
+    exit 1
+}
+
+
+# check usage
+[ -n "$1" ] && [ -n "$2" ] || die "Usage: emergence-read-file <site-handle> <site-file-path>"
+
+
+# determine location of this script
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+
+# execute php script
+cat <<'END_OF_PHP' | "${DIR}/shell" "$1" --stdin "$2"
+<?php
+
+$node = Site::resolvePath($argv[1]);
+
+if (!$node) {
+    error_log('emergence-read-file: cannot read \''.$argv[1].'\': No such file');
+    exit(1);
+}
+
+readfile($node->RealPath);
+exit(0);
+
+END_OF_PHP
+
+
diff --git a/bin/resolve-site b/bin/resolve-site
new file mode 100755
index 0000000..1c8be6e
--- /dev/null
+++ b/bin/resolve-site
@@ -0,0 +1,45 @@
+#!/bin/bash
+
+die () {
+    echo >&2 "emergence-resolve-site: $@"
+    exit 1
+}
+
+
+# check usage
+[ -n "$1" ] || die "Usage: emergence-resolve-site <hostname>"
+[ -d "/emergence/sites" ] || die "/emergence/sites not found"
+
+
+# determine location of this script
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+
+# determine path to underscore
+UNDERSCORE="$DIR/../node_modules/.bin/underscore"
+
+
+# search sites
+pushd /emergence/sites > /dev/null
+for SITE_DIR in `find . -maxdepth 1 ! -path . -type d`; do
+    SITE_HANDLE="$(basename ${SITE_DIR})"
+    SITE_HOSTNAMES="$(sudo cat ${SITE_DIR}/site.json | $UNDERSCORE process '(data.hostnames||[]).concat([data.primary_hostname]).filter(x=>x)' --outfmt text)"
+
+    for SITE_HOSTNAME in $SITE_HOSTNAMES; do
+        if [[ "${1}" == $SITE_HOSTNAME ]]; then # NOT MATCHING WILDCARD
+            echo "${SITE_HANDLE}"
+            exit 0
+        fi
+    done
+done
+popd > /dev/null
+
+
+# return failure if no match found
+exit 1
diff --git a/bin/shell b/bin/shell
index 588c56d..44810ac 100755
--- a/bin/shell
+++ b/bin/shell
@@ -57,6 +57,10 @@ fi
 
 # execute interactive shell
 TERM=$TERM sudo -E -u www-data -g www-data php -d auto_prepend_file=$autoPrependScript -d apc.enable_cli=on -d memory_limit=-1 $INPUT_ARGS
+SCRIPT_STATUS=$?
 
 # clean up
 rm $autoPrependScript;
+
+# relay exit status of php script
+exit $SCRIPT_STATUS
diff --git a/bin/write-file b/bin/write-file
new file mode 100755
index 0000000..f984791
--- /dev/null
+++ b/bin/write-file
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+die () {
+    echo >&2 "$@"
+    exit 1
+}
+
+
+# check usage
+[ -n "$1" ] && [ -n "$2" ] || die "Usage: emergence-write-file <site-handle> <site-file-path> [host-file-path]"
+
+
+# determine location of this script
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+
+
+
+# read stdin to tmp
+if [ -z "${3}" ]; then
+    # determine path to underscore
+    UNDERSCORE="$DIR/../node_modules/.bin/underscore"
+
+    # read application group name
+    APP_GROUP="$(sudo cat /emergence/config.json | $UNDERSCORE extract --outfmt text group)"
+    INPUT_FILE="$(mktemp)"
+    chgrp "${APP_GROUP}" "${INPUT_FILE}"
+    chmod g+r "${INPUT_FILE}"
+
+    cat - > "${INPUT_FILE}"
+elif [ ! -f "${3}" ]; then
+    die "Input file ${3} not found"
+else
+    INPUT_FILE="${3}"
+fi
+
+
+# execute php script
+cat <<'END_OF_PHP' | exec "${DIR}/shell" "${1}" --stdin "${2}" "${INPUT_FILE}"
+<?php
+
+try {
+    Emergence_FS::importFile($argv[2], $argv[1]);
+    exit(0);
+} catch (Exception $e) {
+    error_log('emergence-write-file: failed to delete file from VFS: '.$e->getMessage());
+    exit(1);
+}
+
+END_OF_PHP
+
+
diff --git a/kernel-lib/server.js b/kernel-lib/server.js
index 1d715a8..14930fa 100644
--- a/kernel-lib/server.js
+++ b/kernel-lib/server.js
@@ -7,7 +7,8 @@ var http = require('http'),
     url = require('url'),
     static = require('node-static'),
     events = require('events'),
-    nodeCleanup = require('node-cleanup');
+    nodeCleanup = require('node-cleanup'),
+    httpAuth = require('http-auth');
 
 
 exports.createServer = function (paths, options) {
@@ -41,9 +42,9 @@ util.inherits(Server, events.EventEmitter);
 
 Server.prototype.start = function () {
     // create authenticator
-    this.httpAuth = require('http-auth')({
-        authRealm: 'Emergence Node Management',
-        authFile: '/emergence/admins.htpasswd'
+    const basicAuth = httpAuth.basic({
+        realm: 'Emergence Node Management',
+        file: '/emergence/admins.htpasswd'
     });
 
     // create static fileserver
@@ -58,7 +59,7 @@ Server.prototype.start = function () {
 
         this.webProtocol = 'https';
     } else {
-        this.webServer = http.createServer(this.handleWebRequest.bind(this)).listen(this.options.port, this.options.host);
+        this.webServer = http.createServer(basicAuth, this.handleRequest.bind(this)).listen(this.options.port, this.options.host);
 
         this.webProtocol = 'http';
     }
@@ -72,14 +73,6 @@ Server.prototype.start = function () {
     console.log('Management server listening on '+this.webProtocol+'://'+this.options.host+':'+this.options.port);
 };
 
-Server.prototype.handleWebRequest = function (request, response) {
-    var me = this;
-
-    me.httpAuth.apply(request, response, function () {
-        me.handleRequest(request, response);
-    });
-};
-
 Server.prototype.handleRequest = function (request, response) {
     var me = this;
 
diff --git a/kernel-lib/services/mysql.js b/kernel-lib/services/mysql.js
index f835738..aebe8df 100644
--- a/kernel-lib/services/mysql.js
+++ b/kernel-lib/services/mysql.js
@@ -41,7 +41,7 @@ function MysqlService (name, controller) {
 
     // check binary version
     console.log(me.name+': detecting mysqld version...');
-    versionMatch = shell.exec(me.options.execPath+' --version').output.match(/mysqld\s+Ver\s+(\d+(\.\d+)*)(-MariaDB)?/);
+    versionMatch = shell.exec(me.options.execPath+' --version').stdout.match(/mysqld\s+Ver\s+(\d+(\.\d+)*)(-MariaDB)?/);
 
     if (!versionMatch) {
         throw 'Failed to detect mysql version';
diff --git a/kernel-lib/sites.js b/kernel-lib/sites.js
index 57b0810..5cb96ca 100644
--- a/kernel-lib/sites.js
+++ b/kernel-lib/sites.js
@@ -4,8 +4,8 @@ var _ = require('underscore'),
     path = require('path'),
     util = require('util'),
     events = require('events'),
-    posix = require('posix'),
     spawn = require('child_process').spawn,
+    shell = require('shelljs'),
     hostile = require('hostile'),
     phpShellScript = path.resolve(__dirname, '../bin/shell');
 
@@ -26,8 +26,8 @@ function Sites (config) {
     me.options = options || {};
     me.options.sitesDir = me.options.sitesDir || '/emergence/sites';
     me.options.localhost = me.options.localhost || '127.0.0.1';
-    me.options.dataUID = me.options.dataUID || posix.getpwnam(config.user).uid;
-    me.options.dataGID = me.options.dataGID || posix.getgrnam(config.group).gid;
+    me.options.dataUID = parseInt(me.options.dataUID || shell.exec(`id -u ${config.user}`).stdout.trim(), 10);
+    me.options.dataGID = parseInt(me.options.dataGID || shell.exec(`getent group ${config.group}`).stdout.split(':')[2], 10);
     me.options.dataMode = me.options.dataMode || '775';
 
     // create required directories
diff --git a/package-lock.json b/package-lock.json
new file mode 100644
index 0000000..e597869
--- /dev/null
+++ b/package-lock.json
@@ -0,0 +1,904 @@
+{
+  "name": "emergence",
+  "version": "1.1.0",
+  "lockfileVersion": 1,
+  "requires": true,
+  "dependencies": {
+    "JSONSelect": {
+      "version": "0.4.0",
+      "integrity": "sha1-oI7cxn6z/L6Z7WMIVTRKDPKCu40=",
+      "optional": true
+    },
+    "ansi-regex": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-3.0.0.tgz",
+      "integrity": "sha1-7QMXwyIGT3lGbAKWa922Bas32Zg="
+    },
+    "apache-crypt": {
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/apache-crypt/-/apache-crypt-1.2.1.tgz",
+      "integrity": "sha1-1vxyqm0n2ZyVqU/RiNcx7v/6Zjw=",
+      "requires": {
+        "unix-crypt-td-js": "^1.0.0"
+      }
+    },
+    "apache-md5": {
+      "version": "1.1.2",
+      "resolved": "https://registry.npmjs.org/apache-md5/-/apache-md5-1.1.2.tgz",
+      "integrity": "sha1-7klza2ObTxCLbp5ibG2pkwa0FpI="
+    },
+    "balanced-match": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.0.tgz",
+      "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c="
+    },
+    "bcryptjs": {
+      "version": "2.4.3",
+      "resolved": "https://registry.npmjs.org/bcryptjs/-/bcryptjs-2.4.3.tgz",
+      "integrity": "sha1-mrVie5PmBiH/fNrF2pczAn3x0Ms="
+    },
+    "brace-expansion": {
+      "version": "1.1.11",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz",
+      "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==",
+      "requires": {
+        "balanced-match": "^1.0.0",
+        "concat-map": "0.0.1"
+      }
+    },
+    "camelcase": {
+      "version": "5.3.1",
+      "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-5.3.1.tgz",
+      "integrity": "sha512-L28STB170nwWS63UjtlEOE3dldQApaJXZkOI1uMFfzf3rRuPegHaHesyee+YxQ+W6SvRDQV6UrdOdRiR153wJg=="
+    },
+    "cliui": {
+      "version": "4.1.0",
+      "resolved": "https://registry.npmjs.org/cliui/-/cliui-4.1.0.tgz",
+      "integrity": "sha512-4FG+RSG9DL7uEwRUZXZn3SS34DiDPfzP0VOiEwtUWlE+AR2EIg+hSyvrIgUUfhdgR/UkAeW2QHgeP+hWrXs7jQ==",
+      "requires": {
+        "string-width": "^2.1.1",
+        "strip-ansi": "^4.0.0",
+        "wrap-ansi": "^2.0.0"
+      },
+      "dependencies": {
+        "string-width": {
+          "version": "2.1.1",
+          "resolved": "https://registry.npmjs.org/string-width/-/string-width-2.1.1.tgz",
+          "integrity": "sha512-nOqH59deCq9SRHlxq1Aw85Jnt4w6KvLKqWVik6oA9ZklXLNIOlqg4F2yrT1MVaTjAqvVwdfeZ7w7aCvJD7ugkw==",
+          "requires": {
+            "is-fullwidth-code-point": "^2.0.0",
+            "strip-ansi": "^4.0.0"
+          }
+        }
+      }
+    },
+    "code-point-at": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/code-point-at/-/code-point-at-1.1.0.tgz",
+      "integrity": "sha1-DQcLTQQ6W+ozovGkDi7bPZpMz3c="
+    },
+    "coffee-script": {
+      "version": "1.12.7",
+      "integrity": "sha1-wF2uDLeVkdBbMHCoQzqYyaiczFM=",
+      "optional": true
+    },
+    "colors": {
+      "version": "1.3.3",
+      "resolved": "https://registry.npmjs.org/colors/-/colors-1.3.3.tgz",
+      "integrity": "sha512-mmGt/1pZqYRjMxB1axhTo16/snVZ5krrKkcmMeVKxzECMMXoCgnvTPp10QgHfcbQZw8Dq2jMNG6je4JlWU0gWg=="
+    },
+    "concat-map": {
+      "version": "0.0.1",
+      "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz",
+      "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s="
+    },
+    "cross-spawn": {
+      "version": "6.0.5",
+      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-6.0.5.tgz",
+      "integrity": "sha512-eTVLrBSt7fjbDygz805pMnstIs2VTBNkRm0qxZd+M7A5XDdxVRWO5MxGBXZhjY4cqLYLdtrGqRf8mBPmzwSpWQ==",
+      "requires": {
+        "nice-try": "^1.0.4",
+        "path-key": "^2.0.1",
+        "semver": "^5.5.0",
+        "shebang-command": "^1.2.0",
+        "which": "^1.2.9"
+      },
+      "dependencies": {
+        "semver": {
+          "version": "5.7.0",
+          "resolved": "https://registry.npmjs.org/semver/-/semver-5.7.0.tgz",
+          "integrity": "sha512-Ya52jSX2u7QKghxeoFGpLwCtGlt7j0oY9DYb5apt9nPlJ42ID+ulTXESnt/qAQcoSERyZ5sl3LDIOw0nAn/5DA=="
+        }
+      }
+    },
+    "decamelize": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/decamelize/-/decamelize-1.2.0.tgz",
+      "integrity": "sha1-9lNNFRSCabIDUue+4m9QH5oZEpA="
+    },
+    "denque": {
+      "version": "1.4.1",
+      "resolved": "https://registry.npmjs.org/denque/-/denque-1.4.1.tgz",
+      "integrity": "sha512-OfzPuSZKGcgr96rf1oODnfjqBFmr1DVoc/TrItj3Ohe0Ah1C5WX5Baquw/9U9KovnQ88EqmJbD66rKYUQYN1tQ=="
+    },
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+      "integrity": "sha1-R1OT/56RR5rqYtyvDKPRSYOn+0A="
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+      "requires": {
+        "emoji-regex": "^7.0.1",
+        "is-fullwidth-code-point": "^2.0.0",
+        "strip-ansi": "^5.1.0"
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+          "requires": {
+            "ansi-regex": "^4.1.0"
+          }
+        }
+      }
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+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-4.0.0.tgz",
+      "integrity": "sha1-qEeQIusaw2iocTibY1JixQXuNo8=",
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+      "integrity": "sha1-JNyWnJNvHQ7hHT51FKMtpJGS8JI=",
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+        "JSONSelect": "*",
+        "coffee-script": "*",
+        "commander": "1.0.5",
+        "msgpack": "*",
+        "underscore": "1.8.3",
+        "underscore.string": "3.2.3"
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+      "integrity": "sha1-HAgkFQSBvHoB1J6Y8exmjYJBLzs="
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+      "integrity": "sha512-yXJmeNaw3DnnKAOKJE51sL/ZaYfWJRl1pK9dr19YFCu0ObS231AB1/LbqTKRAQ5kw8A90rA6fr4riOUpTZvQZA=="
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+      "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
+      "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
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+    },
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+      "integrity": "sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI="
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+      "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.2.2.tgz",
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+      "requires": {
+        "cliui": "^4.0.0",
+        "find-up": "^3.0.0",
+        "get-caller-file": "^2.0.1",
+        "os-locale": "^3.1.0",
+        "require-directory": "^2.1.1",
+        "require-main-filename": "^2.0.0",
+        "set-blocking": "^2.0.0",
+        "string-width": "^3.0.0",
+        "which-module": "^2.0.0",
+        "y18n": "^4.0.0",
+        "yargs-parser": "^13.0.0"
+      }
+    },
+    "yargs-parser": {
+      "version": "13.0.0",
+      "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.0.0.tgz",
+      "integrity": "sha512-w2LXjoL8oRdRQN+hOyppuXs+V/fVAYtpcrRxZuF7Kt/Oc+Jr2uAcVntaUTNT6w5ihoWfFDpNY8CPx1QskxZ/pw==",
+      "requires": {
+        "camelcase": "^5.0.0",
+        "decamelize": "^1.2.0"
+      }
+    }
+  }
+}
diff --git a/package.json b/package.json
index ab9daca..bf72bfb 100644
--- a/package.json
+++ b/package.json
@@ -1,21 +1,20 @@
 {
   "name": "emergence",
   "preferGlobal": true,
-  "version": "1.0.7",
+  "version": "1.1.0",
   "license": "MIT",
   "dependencies": {
-    "hostile": "^1.0.2",
-    "http-auth": "1.2.7",
-    "mysql2": "^1.5.1",
-    "node-cleanup": "^2.1.2",
-    "node-phpfpm": "^1.0.1",
-    "node-static": "git+https://github.com/JarvusInnovations/node-static.git",
-    "posix": "^4.0.2",
-    "semver": "^5.1.0",
-    "shelljs": "^0.5.3",
-    "underscore": "1.3.x",
-    "underscore-cli": "^0.2.19",
-    "yargs": "^11.0.0"
+    "hostile": "^1.3.x",
+    "http-auth": "^3.2.x",
+    "mysql2": "^1.6.x",
+    "node-cleanup": "^2.1.x",
+    "node-phpfpm": "^1.0.x",
+    "node-static": "^0.7.x",
+    "semver": "^6.0.x",
+    "shelljs": "^0.8.x",
+    "underscore": "^1.9.x",
+    "underscore-cli": "^0.2.x",
+    "yargs": "^13.2.x"
   },
   "bin": {
     "emergence-kernel": "./bin/kernel",
@@ -24,7 +23,13 @@
     "emergence-su": "./bin/su",
     "emergence-create-site": "./bin/create-site.sh",
     "emergence-mysql-shell": "./bin/mysql-shell",
-    "emergence-fire-event": "./bin/fire-event"
+    "emergence-fire-event": "./bin/fire-event",
+    "emergence-read-file": "./bin/read-file",
+    "emergence-write-file": "./bin/write-file",
+    "emergence-delete-file": "./bin/delete-file",
+    "emergence-resolve-site": "./bin/resolve-site",
+    "emergence-certbot-auth": "./bin/certbot-auth",
+    "emergence-certbot-cleanup": "./bin/certbot-cleanup"
   },
   "repository": {
     "type": "git",
diff --git a/php-bootstrap/lib/HttpProxy.class.php b/php-bootstrap/lib/HttpProxy.class.php
index 638405b..be620e7 100644
--- a/php-bootstrap/lib/HttpProxy.class.php
+++ b/php-bootstrap/lib/HttpProxy.class.php
@@ -62,7 +62,7 @@ public static function relayRequest($options)
         }
 
         // get cookies
-        if (!isset($options['cookies'])) {
+        if (!isset($options['cookies']) && !empty($_SERVER['HTTP_COOKIE'])) {
             $options['cookies'] = $_SERVER['HTTP_COOKIE'];
         }
 
diff --git a/php-bootstrap/lib/Site.class.php b/php-bootstrap/lib/Site.class.php
index 43d129e..3775d25 100644
--- a/php-bootstrap/lib/Site.class.php
+++ b/php-bootstrap/lib/Site.class.php
@@ -194,43 +194,12 @@ public static function handleRequest()
             return Emergence::handleRequest();
         }
 
-        // TEMPORARY: bypass routing for some scripts
-        // TODO: delete this
-        foreach (['develop', 'editor', 'app'] AS $bypassRoute) {
-            if (static::$pathStack[0] == $bypassRoute) {
-                static::$resolvedPath = [array_shift(static::$pathStack)];
-                return static::executeScript(static::resolvePath("site-root/$bypassRoute.php"));
-            }
-        }
-
-        // TODO: delete this too
-        if (static::$pathStack[0] == 'site-admin') {
-            if (count(static::$pathStack) > 1) {
-                static::$resolvedPath = [array_shift(static::$pathStack), array_shift(static::$pathStack)];
-                return static::executeScript(static::resolvePath("site-root/site-admin/".static::$resolvedPath[1].".php"));
-            } else {
-                static::$resolvedPath = [array_shift(static::$pathStack)];
-                return static::executeScript(static::resolvePath("site-root/site-admin/_index.php"));
-            }
-        }
-
-        // header('Content-Type: text/plain');
-
-        // printf("Getting result for pathStack: %s\n", implode('/', static::$pathStack));
-
         // resolve request path against site-root filesystem
         $pathResult = static::getRequestPathResult(static::$pathStack);
         static::$resolvedNode = $pathResult['resolvedNode'];
         static::$resolvedPath = $pathResult['resolvedPath'];
         static::$pathStack = $pathResult['pathStack'];
 
-        // print_r([
-        //     '$pathResult[resolvedNode]' => sprintf('%s:%s', $pathResult['resolvedNode']->Class, $pathResult['resolvedNode']->FullPath),
-        //     '$pathResult[resolvedPath]' => implode('/', $pathResult['resolvedPath']),
-        //     '$pathResult[pathStack]' => implode('/', $pathResult['pathStack']),
-        //     '$pathResult[searchPath]' => implode('/', $pathResult['searchPath'])
-        // ]);
-
         // bail now if no node found
         if (!static::$resolvedNode) {
             return static::respondNotFound();
@@ -296,32 +265,20 @@ public static function getRequestPathResult($path)
             $path = static::splitPath($path);
         }
 
-        // header('Content-Type: text/plain');
-        // printf("getRequestPathResult(%s)\n", implode('/', $path));
-
         // rewrite empty path to default page
         if (empty($path[0]) && static::$defaultPage) {
             $path = array(static::$defaultPage);
         }
 
         // crawl down path stack until a handler is found
-        // printf("while (\$handle = array_shift(%s))\n", implode(',', $path));
         $searchPath = array('site-root');
         while ($handle = array_shift($path)) {
-
-            // printf(
-            //     "\n\t\$searchPath=%s\n\t\$handle=%s\n\t\$path=.../%s\n",
-            //     implode('/', $searchPath),
-            //     $handle, implode('/', $path)
-            // );
-
             $foundNode = null;
 
             // if path component doesn't already end in .php, check for a .php match first
             if (substr($handle, -4) != '.php') {
                 array_push($searchPath, $handle.'.php');
                 $foundNode = static::resolvePath($searchPath);
-                // printf("\t\t%s\t%s\n", $foundNode ? 'matched' : 'missed', implode('/', $searchPath));
                 array_pop($searchPath);
 
                 // don't match a collection as a script
@@ -334,7 +291,6 @@ public static function getRequestPathResult($path)
             if (!$foundNode) {
                 array_push($searchPath, $handle);
                 $foundNode = static::resolvePath($searchPath);
-                // printf("\t\t%s\t%s\n", $foundNode ? 'matched' : 'missed', implode('/', $searchPath));
                 array_pop($searchPath);
             }
 
@@ -358,8 +314,6 @@ public static function getRequestPathResult($path)
             $searchPath[] = $foundNode->Handle;
         }
 
-        // print("\nDone while.\n\n");
-
         return [
             'resolvedNode' => $resolvedNode,
             'resolvedPath' => $resolvedPath,