Improve DOCX environment variable documentation

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README.md

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+# Output directory containing the formatted manuscript
+
+The [`gh-pages`](https://github.com/greenelab/jake_dissertation/tree/gh-pages) branch hosts the contents of this directory at <https://greenelab.github.io/jake_dissertation/>.
+The permalink for this webpage version is <https://greenelab.github.io/jake_dissertation/v/8c1a803748961dcf6b7e8ed4d5ec8f8ce6d5a2a9/>.
+To redirect to the permalink for the latest manuscript version at anytime, use the link <https://greenelab.github.io/jake_dissertation/v/freeze/>.
+
+## Files
+
+This directory contains the following files, which are mostly ignored on the `main` branch:
+
++ [`index.html`](index.html) is an HTML manuscript.
++ [`manuscript.pdf`](manuscript.pdf) is a PDF manuscript.
+
+The `v` directory contains directories for each manuscript version.
+In general, a version is identified by the commit hash of the source content that created it.
+
+### Timestamps
+
+The `*.ots` files in version directories are OpenTimestamps which can be used to verify manuscript existence at or before a given time.
+[OpenTimestamps](https://opentimestamps.org/) uses the Bitcoin blockchain to attest to file hash existence.
+The `deploy.sh` script run during continuous deployment creates the `.ots` files through its `manubot webpage` call.
+There is a delay before timestamps get confirmed by a Bitcoin block.
+Therefore, `.ots` files are initially incomplete and should be upgraded at a later time, so that they no longer rely on the availability of a calendar server to verify.
+The `manubot webpage` call during continuous deployment identifies files matched by `webpage/v/**/*.ots` and attempts to upgrade them.
+You can also manually upgrade timestamps, by running the following in the `gh-pages` branch:
+
+```shell
+ots upgrade v/*/*.ots
+rm v/*/*.ots.bak
+git add v/*/*.ots
+```
+
+Verifying timestamps with the `ots verify` command requires running a local bitcoin node with JSON-RPC configured, at this time.
+
+## Source
+
+The manuscripts in this directory were built from
+[`8c1a803748961dcf6b7e8ed4d5ec8f8ce6d5a2a9`](https://github.com/greenelab/jake_dissertation/commit/8c1a803748961dcf6b7e8ed4d5ec8f8ce6d5a2a9).