fix(setup): don't re-copy examples on setup re-runs

User report: `example-source.md` was being copied back into the
workspace every time `thesis setup` ran. That meant a user who
deleted the example on purpose had it restored uninvited.

Root cause: Step 5 (Copy examples) treated every invocation as a
first run. Non-interactive / quickstart modes auto-copied; the
interactive prompt defaulted to Yes; the `_copy_examples` helper
silently skipped existing files (so the re-copy only created files
the user had since deleted, which is exactly the surprise they
reported).

Changes
  - setup() now captures `first_run = not .env.exists()` at entry.
  - Step 5 branching:
      * `--skip-examples`  → always skip
      * `--with-examples`  → always copy (new flag; explicit opt-in
                             for re-runs)
      * `--overwrite-examples` → now implies copy too, so the flag
                                 isn't a silent no-op on re-runs
      * non-interactive / quickstart on a re-run → skip with a clear
                                 message naming the escape hatch
      * interactive on a re-run → prompt defaults to No and the
                                 wording says why ("you've run setup
                                 before; default is No so deleted
                                 examples don't come back")
      * first run everywhere → behaves as before (copy by default)

Tests (1 new, 1 rewritten; 271 total passing)
  - test_second_run_skips_examples_by_default: locks in that
    a re-run without flags neither copies nor re-creates deleted
    examples, and the output names `--with-examples`.
  - test_second_run_with_examples_flag_copies_and_reports_already_present:
    explicit opt-in path still works.
  - Regression smoke verified manually: deleted
    research/raw/example-source.md, re-ran `thesis setup`, file
    stayed gone.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: NikitasT2003

src/thesis_agent/cli.py

@@ -223,6 +223,10 @@ def setup(
         False, "--overwrite-examples",
         help="Replace example files in the workspace even if they already exist.",
     ),
+    with_examples: bool = typer.Option(
+        False, "--with-examples",
+        help="Copy examples even on a re-run of setup (by default examples are only offered on first run).",
+    ),
     quickstart: bool = typer.Option(
         False, "--quickstart", help="Accept sensible defaults for every prompt.",
     ),
@@ -244,6 +248,10 @@ def setup(
     )
 
     p = paths()
+    # `.env` existing is our signal that setup has run here before — we don't
+    # re-offer examples on re-runs so users who deleted them don't have them
+    # come back uninvited. `--with-examples` forces the copy on a re-run.
+    first_run = not p.env_file.exists()
 
     try:
         # Step 1: Provider ---------------------------------------------------
@@ -348,14 +356,33 @@ def setup(
         _step(5, "Copy examples (optional)")
         if skip_examples:
             copy_ex = False
+        elif with_examples or overwrite_examples:
+            # Explicit opt-in — copy regardless of first-run status.
+            # `--overwrite-examples` implies opt-in; otherwise it would be a
+            # no-op on re-runs (which would be surprising).
+            copy_ex = True
         elif non_interactive or quickstart:
-            copy_ex = not skip_examples
+            # Headless: only auto-copy on first run. Once the user has run
+            # setup before (i.e. .env already exists), we assume they either
+            # already accepted examples the first time OR chose to delete them.
+            copy_ex = first_run
+            if not copy_ex:
+                console.print(
+                    "  [dim]re-run detected — skipping examples. "
+                    "Pass [cyan]--with-examples[/] to copy them anyway.[/]"
+                )
         else:
+            prompt = (
+                "Copy example sources + sample style essay? (recommended for first run)"
+                if first_run
+                else "Copy example sources again? (you've run setup before; "
+                     "default is No so deleted examples don't come back)"
+            )
             try:
                 copy_ex = _ask(
                     questionary.confirm,
-                    "Copy example sources + sample style essay? (recommended for first run)",
-                    default=True,
+                    prompt,
+                    default=first_run,
                 )
             except _Cancelled:
                 copy_ex = False

tests/test_copy_examples.py

@@ -97,15 +97,27 @@ def test_first_run_says_copied_N(self, ws: Path):
         # Should name at least one new file
         assert "new" in result.stdout
 
-    def test_second_run_says_already_present(self, ws: Path):
+    def test_second_run_skips_examples_by_default(self, ws: Path):
+        """On re-run, we must NOT re-copy examples (user may have deleted
+        them deliberately). The wizard should tell them what happened and
+        how to force a copy."""
         self._run_setup()
         result = self._run_setup()
         assert result.exit_code == 0
-        # Must NOT mislead with "copied 0"
+        # Must not mislead with "copied 0"
+        assert "copied 0" not in result.stdout
+        # Must announce the skip + the escape hatch
+        assert "re-run detected" in result.stdout or "skipping examples" in result.stdout
+        assert "--with-examples" in result.stdout
+
+    def test_second_run_with_examples_flag_copies_and_reports_already_present(self, ws: Path):
+        """If user explicitly passes --with-examples on a re-run, we attempt
+        the copy and report honestly (already-present since they're already there)."""
+        self._run_setup()
+        result = self._run_setup(["--with-examples"])
+        assert result.exit_code == 0
         assert "copied 0" not in result.stdout
-        # Must explain the real state
         assert "already in your workspace" in result.stdout
-        # Must point to the escape hatch
         assert "--overwrite-examples" in result.stdout
 
     def test_overwrite_flag_replaces_and_reports(self, ws: Path):