fix(#1836): count prefixed milestone phase dirs (#1844)

* fix(#1836): count prefixed milestone phase dirs

* chore(#1836): add changeset fragment

src/init.cts

@@ -64,7 +64,7 @@ const {
   extractCurrentMilestone,
 } = roadmapParser;
 const { pathExistsInternal, generateSlugInternal, toPosixPath } = coreUtils;
-const { normalizePhaseName, phaseTokenMatches } = phaseId;
+const { normalizePhaseName, phaseTokenMatches, stripProjectCodePrefix } = phaseId;
 const { pruneOrphanedWorktrees } = worktreeSafety;
 
 const {
@@ -1204,7 +1204,7 @@ function cmdInitMilestoneOp(cwd: string, raw: boolean): void {
     const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
     for (const e of entries) {
       if (!e.isDirectory()) continue;
-      const m = e.name.match(/^(\d+[A-Z]?(?:\.\d+)*)/);
+      const m = stripProjectCodePrefix(e.name).match(/^(\d+[A-Z]?(?:\.\d+)*)/);
       if (!m) continue;
       diskPhaseDirs.set(canonicalizePhase(m[1]), e.name);
     }