[JacobStephens2]

Summary

thirdshift setup over an existing User config now edits it in place with toml_edit (pure Rust, so it builds under musl per ADR-0003), instead of leaving it as it was.

 setup
   read the User config
   none → write DEFAULTS
   parse it as a Run would → refuse: exit 1, file untouched
-  "already set up"
+  complete(text)
+    missing key in an existing section → appended at the end of that section, with its comment from DEFAULTS
+    missing section                    → appended after the file's last line
+    no email.to and no "# to =" line   → the commented-out example goes just above email.from
+  unchanged → say so, write nothing
+  changed   → replace the file through a temp file, keeping its permissions

Before, with a partial User config:

# My machine
[merge]
always = true   # trust

[email]
to = "me@example.com"  # inbox

After thirdshift setup </dev/null:

# My machine
[merge]
always = true   # trust

[email]
to = "me@example.com"  # inbox
always = false                  # every Run sends a Run notification, without the email word; default false
from = "onboarding@resend.dev"  # the sender; default onboarding@resend.dev, which only delivers to your Resend account's address

[launch]
pull = false     # every Run first fast-forwards your checkout of the Base branch; default false

[logs]
dir = "~/.thirdshift/logs"   # where session logs go; default ~/.thirdshift/logs

Evidence

• Before: on main, setup over an existing User config returns "already set up" after parsing it and writes nothing, so a partial file gains none of its missing keys.
  After: cargo test passes in full, clippy is clean, and tests/setup.rs has 10 of 10 passing, including:
  • a partial config keeps its values and hand-written comments, and gains every missing key with its comment
  • a complete, hand-edited config is left byte for byte as it was
  • invalid TOML, an unknown key and a wrongly typed value each exit 1 with the same stderr a Run gives, and the file is unchanged
  • a Run on the completed file is still a Merge run and still writes its logs to the custom logs.dir
  • running setup twice adds the commented-out email.to line only once
• Unit tests on complete cover dotted keys, inline tables, no trailing newline, and trailing comments. They also check that a Run parses the result with the settings it had before, and that running complete a second time changes nothing.

Merge Danger

Door: two-way

This rewrites users' files, but only by adding lines, and it never rewrites a file that is already complete. Reverting the PR restores the old behavior.

Blast Radius: small

Only thirdshift setup over an existing User config is affected. A Run, email-test, update, version and help don't change. The only new dependency is toml_edit.

Unaddressed findings

Standards

• The table and inline-table arms repeat the same missing-key loop (Duplicated Code). Skipped: the two insert through different toml_edit APIs and one drops comments, so a closure-taking helper wouldn't make it clearer.
• The email section is special-cased by name (Primitive Obsession). Skipped: email.to is the one key with no default, so the special case is real.
• has_commented_out_email_to rescans the raw text. Partly addressed: it now matches an [email] header exactly. The rescan stays because toml_edit scatters comments across key decor, the next header and the document trailer.
• The same behavior is tested through both the unit and integration seams. Skipped: the integration test covers the acceptance criterion, and the unit tests cover edge cases cheaply.

Spec

• A key added to an inline table gets no comment. Skipped: TOML has no place for a comment inside an inline table. The README and the doc comment now say so.
• Dotted email.* keys don't get the commented-out email.to line. Skipped: it's a rare form and there's no natural place for the line. The keys themselves are still added.
• Adding the commented-out email.to line is scope creep. Skipped: it keeps "the file lists every key the installed version knows" true, and matches the file Setup writes from scratch.
• A comment at the end of a section ends up below the keys added to it. Skipped: this is how toml_edit attaches such comments. The comment is kept, and the settings and their order are unchanged.
• Missing sections go at the end, not in merge, launch, email, logs order. Skipped: that order is for new files. Inserting sections between the user's own would move their text.

Closes #128

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