After searching on the PrismJS Github, I discovered that they have a Normalize Whitespace plugin that trims all leading and trailing whitespace in a code block. It seems this is the official solution to this issue. I pasted the modifications into my existing prismJS file and linked the plugin in this answer.
Since I originally modified my prismCSS file to adjust to this issue, after adopting the new JS plugin, return all alignments to the default settings, in case line numbers and highlighting don't show up after the fix.
!(function () {
if ("undefined" != typeof Prism) {
var e =
Object.assign ||
function (e, t) {
for (var n in t) t.hasOwnProperty(n) && (e[n] = t[n]);
return e;
},
t = {
"remove-trailing": "boolean",
"remove-indent": "boolean",
"left-trim": "boolean",
"right-trim": "boolean",
"break-lines": "number",
indent: "number",
"remove-initial-line-feed": "boolean",
"tabs-to-spaces": "number",
"spaces-to-tabs": "number",
};
(n.prototype = {
setDefaults: function (t) {
this.defaults = e(this.defaults, t);
},
normalize: function (t, n) {
for (var r in (n = e(this.defaults, n))) {
var i = r.replace(/-(\w)/g, function (e, t) {
return t.toUpperCase();
});
"normalize" !== r &&
"setDefaults" !== i &&
n[r] &&
this[i] &&
(t = this[i].call(this, t, n[r]));
}
return t;
},
leftTrim: function (e) {
return e.replace(/^\s+/, "");
},
rightTrim: function (e) {
return e.replace(/\s+$/, "");
},
tabsToSpaces: function (e, t) {
return (t = 0 | t || 4), e.replace(/\t/g, new Array(++t).join(" "));
},
spacesToTabs: function (e, t) {
return (t = 0 | t || 4), e.replace(RegExp(" {" + t + "}", "g"), "\t");
},
removeTrailing: function (e) {
return e.replace(/\s*?$/gm, "");
},
removeInitialLineFeed: function (e) {
return e.replace(/^(?:\r?\n|\r)/, "");
},
removeIndent: function (e) {
var t = e.match(/^[^\S\n\r]*(?=\S)/gm);
return t && t[0].length
? (t.sort(function (e, t) {
return e.length - t.length;
}),
t[0].length ? e.replace(RegExp("^" + t[0], "gm"), "") : e)
: e;
},
indent: function (e, t) {
return e.replace(
/^[^\S\n\r]*(?=\S)/gm,
new Array(++t).join("\t") + "$&"
);
},
breakLines: function (e, t) {
t = !0 === t ? 80 : 0 | t || 80;
for (var n = e.split("\n"), i = 0; i < n.length; ++i)
if (!(r(n[i]) <= t)) {
for (
var o = n[i].split(/(\s+)/g), a = 0, l = 0;
l < o.length;
++l
) {
var s = r(o[l]);
(a += s) > t && ((o[l] = "\n" + o[l]), (a = s));
}
n[i] = o.join("");
}
return n.join("\n");
},
}),
"undefined" != typeof module && module.exports && (module.exports = n),
(Prism.plugins.NormalizeWhitespace = new n({
"remove-trailing": !0,
"remove-indent": !0,
"left-trim": !0,
"right-trim": !0,
})),
Prism.hooks.add("before-sanity-check", function (e) {
var n = Prism.plugins.NormalizeWhitespace;
if (
(!e.settings || !1 !== e.settings["whitespace-normalization"]) &&
Prism.util.isActive(e.element, "whitespace-normalization", !0)
)
if ((e.element && e.element.parentNode) || !e.code) {
var r = e.element.parentNode;
if (e.code && r && "pre" === r.nodeName.toLowerCase()) {
for (var i in (null == e.settings && (e.settings = {}), t))
if (Object.hasOwnProperty.call(t, i)) {
var o = t[i];
if (r.hasAttribute("data-" + i))
try {
var a = JSON.parse(r.getAttribute("data-" + i) || "true");
typeof a === o && (e.settings[i] = a);
} catch (e) {}
}
for (
var l = r.childNodes, s = "", c = "", u = !1, m = 0;
m < l.length;
++m
) {
var f = l[m];
f == e.element
? (u = !0)
: "#text" === f.nodeName &&
(u ? (c += f.nodeValue) : (s += f.nodeValue),
r.removeChild(f),
--m);
}
if (e.element.children.length && Prism.plugins.KeepMarkup) {
var d = s + e.element.innerHTML + c;
(e.element.innerHTML = n.normalize(d, e.settings)),
(e.code = e.element.textContent);
} else
(e.code = s + e.code + c),
(e.code = n.normalize(e.code, e.settings));
}
} else e.code = n.normalize(e.code, e.settings);
});
}
function n(t) {
this.defaults = e({}, t);
}
function r(e) {
for (var t = 0, n = 0; n < e.length; ++n)
e.charCodeAt(n) == "\t".charCodeAt(0) && (t += 3);
return e.length + t;
}
})();
