fix(#3544): restore tilde form for at-refs in the global spec tree (#3551)

* fix(#3544): restore tilde form for at-refs in the global spec tree

A global claude install emitted @$HOME/.claude/gsd-core/references/*.md
in its workflows and references. $HOME does not expand in a Claude Code
@-import - only relative, absolute and ~ are documented, and a controlled
/context test confirmed a $HOME import loads nothing - so 54 includes
across 22 files silently resolved to nothing on a live install.

This is a divergence, not a new bug. #3133 already applies exactly this
correction to skill and command bodies through _applyRuntimeRewrites's
claude case; copyWithPathReplacement, the spec-tree emit path, never had
it. Both now call one exported helper, so the two surfaces cannot drift
apart again.

Deliberately narrower than changing computePathPrefix's return value:
shipped markdown also carries double-quoted "$HOME/.claude/..." shell
invocations, and ~ does not expand inside double quotes, so rewriting the
prefix wholesale would regress #1284. Only @-prefixed references move.

Refs #3544

* fix(#3544): derive the tilde restore from the resolved prefix

Three review findings, one batch.

The restore was hardcoded to the literal .claude directory, so a global
install with --config-dir pointing anywhere else silently no-opped and
reproduced the very defect this fixes. It now derives the tilde form from
the resolved prefix, which also closes the same latent gap in #3133's
original path since both call sites share the helper.

The @-anchor is quote-aware, so a double-quoted shell path is never
rewritten into a form the shell does not expand. Deliberately a lookbehind
rather than a line-start anchor: @-references are documented to work
mid-line, and anchoring would have traded a theoretical bug for a real one.

Found while testing the above: the bare-form rewrites re-matched their own
output whenever a config dir name extends .claude, emitting
.claude-work-work. Guarded with the same negative-lookahead convention
this file already uses to preserve .claude-plugin.

The tests prove the emitted form, never that the host resolves it - no CI
test can - and both the helper and the suite now say so, because an
undocumented verification boundary is how this defect stayed green for its
whole life.

Refs #3544

* test(#3544): acknowledge the tilde-restore emitted drift

The converter change moves 94 emitted paths that no source-file diff can
explain, which is exactly the case the per-PR ack fragment exists for.
Verified before acknowledging rather than after: both trees were built
from real installs and every one of the 211 changed lines across all 94
paths is @$HOME becoming @~, with nothing outside that single kind.

Nine spent entries were pruned from the #3151 and #2658 fragments. Those
paths moved again here, and two ack sources naming one path is a hard
duplicate error rather than last-wins, so the inert entries had to go
before this one could land. Both fragments retain their remaining
entries.

Refs #3544

* chore(#3544): backfill changeset pr number

---------

Co-authored-by: sim <sim@local>

bin/install.js

@@ -7952,8 +7952,20 @@ function copyWithPathReplacement(srcDir, destDir, pathPrefix, runtime, isCommand
         content = content.replace(globalClaudeRegex, pathPrefix);
         content = content.replace(globalClaudeHomeRegex, pathPrefix);
         content = content.replace(localClaudeRegex, `./${dirName}/`);
-        content = content.replace(/~\/\.claude\b/g, pathPrefix.replace(/\/$/, ''));
-        content = content.replace(/\$HOME\/\.claude\b/g, pathPrefix.replace(/\/$/, ''));
+        // #3544 review (Finding 1 fallout): guarded with the SAME
+        // negative-lookahead convention already used at ~:2859-2860 below
+        // ("preserve .claude-plugin and .claudeignore"). A naive `\b` here
+        // is satisfied by ANY non-word character, including '-' — so for a
+        // --config-dir whose name EXTENDS '.claude' (e.g. '.claude-work',
+        // pathPrefix '$HOME/.claude-work/'), this pass re-matched the
+        // '$HOME/.claude' PREFIX of its own slash-form output (lines above)
+        // and re-appended the full prefix, corrupting every emitted path to
+        // '$HOME/.claude-work-work/...'. Harmless no-op for the literal
+        // default '.claude' (self-replace with an identical string), which
+        // is why this went undetected until a non-default config-dir name
+        // was exercised.
+        content = content.replace(/~\/\.claude(?![\w-])/g, pathPrefix.replace(/\/$/, ''));
+        content = content.replace(/\$HOME\/\.claude(?![\w-])/g, pathPrefix.replace(/\/$/, ''));
         content = content.replace(/\.\/\.claude\b/g, `./${dirName}`);
         content = content.replace(/~\/\.qwen\//g, pathPrefix);
         content = content.replace(/\$HOME\/\.qwen\//g, pathPrefix);
@@ -7961,6 +7973,17 @@ function copyWithPathReplacement(srcDir, destDir, pathPrefix, runtime, isCommand
         content = content.replace(/~\/\.hermes\//g, pathPrefix);
         content = content.replace(/\$HOME\/\.hermes\//g, pathPrefix);
         content = content.replace(/\.\/\.hermes\//g, `./${dirName}/`);
+        // #3544: restore @-file-reference lines to the tilde form Claude Code
+        // actually expands — the SAME correction #3133 already applies to
+        // skill/command bodies via _applyRuntimeRewrites's 'claude' case (see
+        // restoreClaudeGlobalAtRefTilde's doc comment in
+        // runtime-artifact-conversion.cts). This is the gsd-core/ spec-tree
+        // emit path, which never had it: every @~/.claude/gsd-core/… include
+        // in a global install's workflows/references tree silently resolved
+        // to nothing (54 includes across 22 files on a live install).
+        if (runtime === 'claude') {
+          content = runtimeArtifactConversion._restoreClaudeGlobalAtRefTilde(content, pathPrefix);
+        }
       }
       content = processAttribution(content, getCommitAttribution(runtime));