Have a look at the HTML Tidy Project: http://www.html-tidy.org/

The granddaddy of HTML tools, with support for modern standards.

There used to be a fork called tidy-html5 which since became the official thing. Here is its GitHub repository.

Tidy is a console application for Mac OS X, Linux, Windows, UNIX, and more. It corrects and cleans up HTML and XML documents by fixing markup errors and upgrading legacy code to modern standards.

For your needs, here is the command line to call Tidy:

tidy inputfile.html

I want a tool that formats HTML files from the command line

– I recommend js-beautify, as suggested in this answer.
I prefer to install it globally:

npm install --global js-beautify

I typically want to format all *.html files in the current folder. ¹

js-beautify *.html --type html --replace --indent-size 1 --max-preserve-newlines 0

The above fulfills all eight requirements of the question, including the three optional ones.

References

• The documentation of the NPM package js-beautify – version 1.14.9
• Answer using js-beautify

js-beautify --type html -r -s 1 -m 0 *.html

First install prettier "globally" using either npm or your Package manager.

Using npm:

npm install -g prettier

To "prettify" CSS using "custom commands" with Geany:

Config - One time only!

1. Edit -> Format -> Send selection to -> Set custom commands
2. Click Add
3. Enter prettier --stdin-filepath temp.css in Command field.
4. Enter CSS in Label
5. Click OK.

Now every time you want to "prettify" CSS:

1. Select the CSS text you want to prettify:
2. Go to / pressEdit -> Format -> Send selection to -> CSS

[recommended] To "prettify" any source code file directly using prettier:

1. npx prettier --write .
2. Read the "Usage" section in the document for more information.

Caution: Prettifying, Beautifying or Formatting your source code files modifies them.

If its something related to pretty printing of file in xml aligned format, xmllint as suggested by @warl0ck is nice & here is what I tried & see:

$cat some.xml
<myRoot> <my-element><my-subelem myAttr="value"/></my-element></myRoot>


$ xmllint --format some.xml
<?xml version="1.0"?>
<myRoot>
  <my-element>
    <my-subelem myAttr="value"/>
  </my-element>
</myRoot>

If you like vim you can invoke its action from the command-line.

echo -e "G=gg\n:wq\n" | vim ./myfile.php 

Warning the above command will modify your file without prompting. Do a backup before.
It's possible to find examples integrated with find to accomplish the same work on a bunch of files ^[0].

Looking beyond it's possible to find a lot of utilities build for this, and this number will continue to grow in time; you can search for their updated versions on internet and you can start for example from:

• Artistic Style ^[1], astyle, for C, C++, C++/CLI, Objective‑C, C# and Java programming languages.
• tidy ^[2] for Html
• IDE solutions invoked by command line starting from kate ^[3] for which there exists just made plug-in; you can built your own indentation scripts ^[4] too, continuing with UniversalIndentGUI ^[5], eclipse ^[5]...

Ok, for anyone else in need of this, I'm recording the suggestions made in this awesome thread (in case that link goes down, as per StackExchange guidelines):

• HTB 2.0 - DOS based - http://www.digital-mines.com/htb/

• Tabifier - supports CSS, HTML and C style syntax (including Javascript) - http://tools.arantius.com/tabifier

• HTML-Kit - a full-featured free HTML editor running on Windows, you need to config TIDY options [Tools /Check code using Tidy /Add new config], uncheck all swithes except "Output only the body content" and "Convert non-breaking space to entities", then go to Actions /Tools /HTML Tidy /Indent Tags or beautify - http://www.chami.com/html-kit/

• SCREEM - only for Linux -

• NetBeans - " After openining an html file with NetBeans, click Source then select Format. That's it. " -

• WebmasterGate's HTML / XHTML Beautifier - Online tool - http://www.webmastergate.com/html-beautifier/

• Aptana Studio (Version 2.0.4) - "Select Edit > Format or press Ctrl-Shift F to format the html code. The format function can be configured from Windows > Preferrences, then select Aptana > Editors > HTML > Formatting, click Edit to add tags which should not take a new line then save it as a new preferrence." -

• UniversalIndentGUI - Uses HTB Beautifier internally - While running Notepad++, go to Plugins > Plugin Manager > Show Plugin Manager, select UniversalIndentGUI from the available list to install it.

• tidy with these options:

(filler text since the markdown engine seems to have problem when code directly follows bullets)

[HTML, XHTML, XML Options]
anchor-as-name:no
doctype:omit
drop-empty-paras:no
fix-backslash:no
fix-bad-comments:no
fix-uri:no
input-xml:yes
join-styles:no
lower-literals:no
preserve-entities:yes
quote-ampersand:no
quote-nbsp:no

[Diagnostics Options]
show-warnings:no

[Pretty Print Options]
indent:yes
indent-spaces:3
tab-size:3

[Miscellaneous Options]
quiet:yes

I'm yet to try out these options (the input-xml: yes and force-output: yes config suggestions to HTML tidy mentioned https://stackoverflow.com/questions/7151180/use-html-tidy-to-just-indent-html-code works for my immediate purpose), will update this answer if I do.

js-beautify also works on HTML.

npm install js-beautify
js-beautify --type html file.html

Notice all this beautifying makes the file size increase substantially. The indentation is great for revision and editing, but not so much for hosting. For that reason, you might find html-minifier equally useful.