fix: preserve Pi workspace aliases and strengthen security regressions

CHANGELOG.md

@@ -1,5 +1,6 @@
 ### 2.12.0 (Unreleased)
 ### Features/Bug Fixes
+* fix(pi): accept scans from symlinked workspace roots while preserving the CLI's checks on symlinks below the workspace. Custom YARA rules loaded with `--yara-rules-dir` cannot use `include`; place each rule directly in the selected directory.
 * fix(taint): key TT1-TT6 taint by lexical scope and follow direct calls to functions and methods defined in the same file, so a tainted variable no longer taints same-named variables in other functions (#799). Message-glob baseline rules keep matching TT findings whose rule and message are unchanged; exact baseline fingerprints are bound to the scanner version and suppress nothing after an upgrade (see docs/SUPPRESSION.md), so they must be regenerated in any case. A TT message changes where the earlier message came from a same-named variable in another scope (it now names the variable, source and line that reach the sink); where a more severe source raises the rule (TT2 to TT3 or TT4, TT4 to TT3, TT2 to TT5 or TT6), and at such a sink, where a weaker finding is subsumed or now cites another variable; and where an identifier longer than 120 characters is now shortened. Re-accept those findings or regenerate the baseline. `match_fingerprint` changes only when the rule does.
 * fix(static): stop code comparisons after removal verbs from reading as unterminated tag-marker directives (#777)
 * fix(baseline): fingerprint every occurrence of a deduplicated finding so the next scan suppresses all of them (#633)

README.md

@@ -782,7 +782,7 @@ Options:
   -f, --format [terminal|json|markdown|sarif]  Output format [default: terminal]
   -o, --output PATH                            Output file path
   --no-llm                                     Skip LLM analysis (static only)
-  --yara-rules-dir PATH                        Extra YARA rules directory
+  --yara-rules-dir PATH                        Extra YARA rules directory (includes disabled)
   -b, --baseline PATH                          Suppress findings listed in a baseline
   --show-suppressed                            List baseline-suppressed findings
   -V, --verbose                                Show detailed progress

extensions/skillspector.ts

@@ -128,9 +128,13 @@ async function approveScanInputs(
     if (!isWithin(resolve(ctx.cwd), path.input) && !isWithin(workspace, path.resolved) && path.resolved !== path.input) {
       aliasRequests.push(readRequest(path.field, path.resolved));
     }
-    // Keep the original target path so the CLI can enforce its no-symlink
-    // input policy. YARA directories are canonicalised by the CLI too.
-    prepared[path.field] = path.field === "target" ? path.input : path.resolved;
+    // Resolve only the workspace prefix; keep child symlinks for the CLI's
+    // no-symlink input checks. YARA directories are canonicalised by the CLI too.
+    prepared[path.field] = path.field === "target"
+      ? isWithin(resolve(ctx.cwd), path.input)
+        ? join(workspace, relative(resolve(ctx.cwd), path.input))
+        : path.input
+      : path.resolved;
   }
   await approve(aliasRequests);
   signal?.throwIfAborted();

tests/unit/test_pi_extension.mjs

@@ -91,6 +91,23 @@ test("uses installed absolute executable and preserves scan arguments without ou
   assert.equal(ctx.calls[0].options.cwd, ctx.workspace);
 });
 
+test("accepts a symlinked workspace without resolving target symlinks below it", async (t) => {
+  const ctx = await setup(t);
+  const alias = join(ctx.root, "workspace-alias");
+  symlinkSync(ctx.workspace, alias);
+  symlinkSync(join(ctx.workspace, "SKILL.md"), join(ctx.workspace, "linked.md"));
+  for (const [target, expected] of [
+    ["./SKILL.md", join(ctx.workspace, "SKILL.md")],
+    [".", ctx.workspace],
+    [join(alias, "SKILL.md"), join(ctx.workspace, "SKILL.md")],
+    ["linked.md", join(ctx.workspace, "linked.md")],
+  ]) {
+    await ctx.scan({ target }, { cwd: alias, hasUI: false });
+    assert.equal(ctx.calls.at(-1).args[1], expected);
+  }
+  assert.equal(ctx.prompts.length, 0);
+});
+
 test("redacts long scanner output without retrying every word character", { timeout: 5000 }, async (t) => {
   const ctx = await setup(t, () => ({
     code: 0,
@@ -209,6 +226,28 @@ test("approves canonical external scope and preserves the CLI target symlink pol
   assert.equal(ctx.calls[0].args.at(-1), join(ctx.root, "rules"));
 });
 
+for (const approveResolved of [true, false]) {
+  test(`external YARA aliases require a second confirmation: approved=${approveResolved}`, async (t) => {
+    let confirmations = 0;
+    const ctx = await setup(t, undefined, async () => ++confirmations === 1 || approveResolved);
+    const rules = join(ctx.root, "rules");
+    const alias = join(ctx.root, "rules-alias");
+    mkdirSync(rules);
+    symlinkSync(rules, alias);
+    const scan = ctx.scan({ yaraRulesDir: "../rules-alias" });
+    if (approveResolved) {
+      await scan;
+      assert.equal(ctx.calls[0].args.at(-1), rules);
+    } else {
+      await assert.rejects(scan, /not approved/);
+      assert.equal(ctx.calls.length, 0);
+    }
+    assert.equal(ctx.prompts.length, 2);
+    assert.ok(ctx.prompts[0].message.includes(JSON.stringify(alias)));
+    assert.ok(ctx.prompts[1].message.includes(JSON.stringify(rules)));
+  });
+}
+
 test("treats local git@ paths as canonical local reads", async (t) => {
   const ctx = await setup(t, undefined, async () => true);
   mkdirSync(join(ctx.workspace, "git@notes"));

tests/unit/test_suppression.py

@@ -252,7 +252,7 @@ def test_transitive_fingerprint_does_not_borrow_lookalike_local_path(delimiter:
 def test_root_lookup_does_not_normalize_a_transitive_content_key() -> None:
     from skillspector.suppression import _component_content
 
-    key = source_content_key("scope", r"..\..\..\x")
+    key = source_content_key(f"external/{'a' * 64}", r"..\..\..\x")
     assert _component_content({key: "remote content"}, './x"]') is None