diff --git a/docs/README.md b/docs/README.md
index 7b8261e6..f8c6042a 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -92,7 +92,7 @@ declarations.
 
 - **What does a specific Rust crate do, on its own terms?** →
   [`crates/`](crates/README.md) — every workspace crate's own
-  `README.md`, one level up from source (hyperhive#3051); the crate
+  `README.md`, one level up from source (#3051); the crate
   itself is still the source of truth, this is just a walkable mirror.
 
 ## Process & conventions
diff --git a/docs/agent-lifecycle/agent-hierarchy.md b/docs/agent-lifecycle/agent-hierarchy.md
index cb8e78ef..47b59cc8 100644
--- a/docs/agent-lifecycle/agent-hierarchy.md
+++ b/docs/agent-lifecycle/agent-hierarchy.md
@@ -4,7 +4,7 @@ Every agent has a place in an operator-editable parent/child tree, used
 to scope which agents can manage which others. This doc covers how
 hive-c0re stores and edits the tree today, the rules that are meant to run on top
 of it once enforcement is finished, and where the manager still gets
-special-cased in the meantime. Tracking issue: hyperhive#361
+special-cased in the meantime. Tracking issue: #361
 (`$HIVE_FORGE_URL/hyperhive/hyperhive/issues/361`).
 
 ## Where the tree lives
diff --git a/docs/crates/README.md b/docs/crates/README.md
index 492dfd52..64ceefd7 100644
--- a/docs/crates/README.md
+++ b/docs/crates/README.md
@@ -3,7 +3,7 @@
 One page per Rust workspace crate — its own `README.md`, unchanged, served
 here for browsing alongside the rest of the docs site. **The crate's own
 `README.md` is the source of truth; nothing here is hand-maintained.**
-`nix/packages/reference-docs.nix` (hyperhive#3051) generates every page at
+`nix/packages/reference-docs.nix` (#3051) generates every page at
 build time straight from the crate's real `README.md`, so it can never
 drift out of sync the way a hand-copied mirror would — edit the crate's
 own README to change what shows up here.
diff --git a/docs/getting-started/setup.md b/docs/getting-started/setup.md
index 4bcf9446..563840fd 100644
--- a/docs/getting-started/setup.md
+++ b/docs/getting-started/setup.md
@@ -95,7 +95,7 @@ store's container reads it, writes the `swarm-controller` policy, enables the
 cert auth method, and creates the `swarm-controller` role that attaches the two.
 
 ⚠️ **This has only run once, and it didn't go all the way through.** The
-first real provision against a live store returned 403 (hyperhive#4124), so
+first real provision against a live store returned 403 (#4124), so
 treat the block above as derived-then-partly-tested rather than proven: the
 grants still come from `-output-policy`, not from a swarm that came up on them.
 What that 403 does _not_ tell you is whether the login or the write was
diff --git a/docs/web-ui/agent.md b/docs/web-ui/agent.md
index a221e3f5..a4b8c66d 100644
--- a/docs/web-ui/agent.md
+++ b/docs/web-ui/agent.md
@@ -85,7 +85,7 @@ structurally rather than for one specific trigger. Two columns:
     `agent_links()` in hive-agent is the single source of truth for
     both. No separate overflow (`⋯`) menu exists any more — it used
     to hold exactly this dashboard link plus a rebuild-container action
-    (mara, hyperhive#3704: "remove rebuild button, move link to
+    (mara, #3704: "remove rebuild button, move link to
     dashboards into links menu") — rebuild had no real discoverability
     need of its own (the dashboard's own R3BU1LD button already covers
     it) so it's gone outright, and the dashboard link moved here,
diff --git a/docs/web-ui/dashboard.md b/docs/web-ui/dashboard.md
index af55c819..bdca1f52 100644
--- a/docs/web-ui/dashboard.md
+++ b/docs/web-ui/dashboard.md
@@ -236,7 +236,7 @@ than reconstructing chrome hive-c0re no longer sends. Settled entries
 render their **full step tree**, not just a bare summary — the wire
 doesn't filter `Done` nodes out.
 
-**State filter (hyperhive#2606).** A row of per-state checkboxes above
+**State filter (#2606).** A row of per-state checkboxes above
 the tree — one per lifecycle state, matching the row glyphs — lets the
 operator narrow which root groups render; unchecking a state re-fetches
 `GET /api/jobq/graph?states=<checked, comma-joined>` rather than
@@ -811,7 +811,7 @@ below).
 
 ### Status badges
 
-**Which single badge (hyperhive#3139):** `ContainerView.failed`
+**Which single badge (#3139):** `ContainerView.failed`
 (systemd `ActiveState=failed` — the unit exhausted its bounded
 restarts and gave up on its own) draws a red `✖ gave up` badge;
 otherwise a plain muted `■ not running` — a container an operator
diff --git a/docs/web-ui/shape.md b/docs/web-ui/shape.md
index ff14032a..27444920 100644
--- a/docs/web-ui/shape.md
+++ b/docs/web-ui/shape.md
@@ -244,7 +244,7 @@ render, `restoreOpenDetails()` re-applies after. Long-content
 drill-ins (file previews, diffs, journald logs) now open in the
 **side panel** (see below) rather than expanding inline. The
 dashboard's own answered-questions history list was the only
-`<details data-restore-key>` consumer and is gone (hyperhive#3721)
+`<details data-restore-key>` consumer and is gone (#3721)
 — `snapshotOpenDetails()` / `restoreOpenDetails()` currently have
 nothing to restore, kept in place for the next collapsible section
 that needs it rather than ripped out along with their one caller.
diff --git a/hive-priv/README.md b/hive-priv/README.md
index c66597e6..ed4cc6a9 100644
--- a/hive-priv/README.md
+++ b/hive-priv/README.md
@@ -55,7 +55,7 @@ sets a per-call cwd, so with `services.hyperhive.c0re.buildSlots > 1`,
 two concurrent calls (any mix of `create`/`update`) could share that one
 `.tmp`: one's `readlink(".tmp")` resolving to the _other's_ build
 output, handing an agent's container the wrong agent's closure — the
-"agent container gets closure of other agent" bug (hyperhive#3312).
+"agent container gets closure of other agent" bug (#3312).
 
 Building the toplevel here and passing the resolved store path via
 `--system-path` for _every_ call means `buildFlake()` never runs at all,
diff --git a/scripts/check-issue-refs.sh b/scripts/check-issue-refs.sh
index 73254b51..a0856d14 100755
--- a/scripts/check-issue-refs.sh
+++ b/scripts/check-issue-refs.sh
@@ -1,47 +1,72 @@
 #!/bin/sh
-# CI lint: flags tracker tags (a hash followed by an issue number) in
-# source comments. The hive convention is prose, not tracker tags, in
-# code (see /knowledge/hive-rules.md) — tags rot, they point at moving
-# targets and leak tracker coupling into the source tree.
+# CI lint, two passes over tracked files. Emits a CI error annotation per
+# hit, exits 1 if either pass finds something. Its own required CI job
+# (branch protection) — a hit blocks merge.
 #
-# Emits a CI error annotation per hit and exits 1 if any tag is found,
-# 0 otherwise. It runs as its own CI job and IS a required check on the
-# forge (branch protection) — a hit blocks merge.
+# 1. Source comments (`.rs .nix .js .ts .tsx .css .html`): flags ANY tracker
+#    tag (hash + issue number) outright — the hive convention is prose, not
+#    tracker tags, in code (/knowledge/hive-rules.md); tags rot. Markdown is
+#    exempt here (prose docs may cite the tracker with a bare `#N`). Pattern:
+#    a hash, 2-5 digits, then non-alphanumeric-or-EOL — skips letter-bearing
+#    hex colours and digit-runs-then-letter (`#24h`). Residual: a pure-
+#    numeric short hex trips it — write the six-digit form to dodge.
 #
-# Scope: tracked *.rs *.nix *.js *.ts *.tsx *.css *.html. Markdown is exempt
-# (prose docs may legitimately cite the tracker). The pattern matches a
-# hash, 2-5 digits, then a non-alphanumeric char or end-of-line. A real
-# tracker tag is never glued to a letter, so the trailing class skips
-# both letter-bearing / 6-8-digit hex colours (the digit run breaks or
-# overruns) and digit-runs followed by a letter — e.g. hash-route
-# fragments like #24h. Residual: a pure-numeric short hex (e.g. three
-# identical digits) trips it — write the six-digit form to dodge.
+# 2. Markdown (`.md`): narrower — only an AMBIGUOUS cross-repo-shaped ref, a
+#    word glued directly to `#N` with no `/` (`hyperhive#1234`). A bare
+#    `#1234` or a qualified `owner/repo#1234` stay legal; only the glued,
+#    unqualified `owner#N` — indistinguishable from a real cross-repo
+#    citation without checking whether `owner` is a live org — gets caught
+#    (the forge's public mirror carries no issue/PR data, so this is dead
+#    weight for a public reader regardless of which repo it meant). The
+#    glued prefix must start lowercase (real org/repo slugs are, see
+#    `hive_types::Ident`) — rules out `PR#4124`/`Hyperhive#1234`. Residual:
+#    an ordinary lowercase word glued to a number (`line#123`) still
+#    matches — no live-allowlist option in a dependency-free script; rare in
+#    practice, same escape hatch as pass 1.
 #
-# Escape hatch: a line containing the marker `lint:allow` is exempt.
-# Reserve it for genuine `#<digits>` that aren't tracker tags — e.g. a
-# `#123` markdown-heading example or hash-prefixed test-input data —
-# and keep a short reason next to the marker. Don't use it to keep a
-# real tracker tag; rewrite those to prose.
+# Escape hatch (both passes): a line with the marker `lint:allow` is exempt.
+# Reserve it for a genuine non-tag hit and keep a short reason next to it —
+# not for a real tracker tag or ambiguous ref, rewrite those instead.
 set -eu
 
-pattern='#[0-9]{2,5}([^0-9a-zA-Z]|$)'
+src_pattern='#[0-9]{2,5}([^0-9a-zA-Z]|$)'
+md_pattern='(^|[^0-9A-Za-z._/-])[a-z][a-z0-9-]*#[0-9]{2,5}([^0-9a-zA-Z]|$)'
 
 # `/dev/null` forces grep to always print a filename prefix, even when
-# xargs hands it a single file. `-r`/`-0` keep it robust to odd paths
-# and an empty file list. Lines carrying the `lint:allow` marker are
-# dropped (legitimate non-tracker `#<digits>`; see the header).
-hits="$(
+# xargs hands it a single file. `-r`/`-0` keep it robust to odd paths and
+# an empty file list. Lines carrying the `lint:allow` marker are dropped
+# (legitimate non-tracker hit; see the header).
+src_hits="$(
   git ls-files -z '*.rs' '*.nix' '*.js' '*.ts' '*.tsx' '*.css' '*.html' \
-    | xargs -0 -r grep -nE "$pattern" /dev/null 2>/dev/null \
+    | xargs -0 -r grep -nE "$src_pattern" /dev/null 2>/dev/null \
+    | grep -v 'lint:allow' || true
+)"
+md_hits="$(
+  git ls-files -z '*.md' \
+    | xargs -0 -r grep -nE "$md_pattern" /dev/null 2>/dev/null \
     | grep -v 'lint:allow' || true
 )"
 
-if [ -n "$hits" ]; then
-  echo "$hits" | while IFS=: read -r file lineno _; do
+count=0
+
+if [ -n "$src_hits" ]; then
+  echo "$src_hits" | while IFS=: read -r file lineno _; do
     printf '::error file=%s,line=%s::tracker tag in source — write prose, not a hash-number tag (see /knowledge/hive-rules.md)\n' "$file" "$lineno"
   done
-  count="$(printf '%s\n' "$hits" | wc -l | tr -d ' ')"
-  printf 'check-issue-refs: %s tracker tag(s) found in source\n' "$count" >&2
+  src_count="$(printf '%s\n' "$src_hits" | wc -l | tr -d ' ')"
+  count=$((count + src_count))
+fi
+
+if [ -n "$md_hits" ]; then
+  echo "$md_hits" | while IFS=: read -r file lineno _; do
+    printf '::error file=%s,line=%s::ambiguous cross-repo reference — a bare `#N` or a fully qualified `owner/repo#N` are fine, but this looks like an unqualified `owner#N`; spell out the repo or clarify in prose\n' "$file" "$lineno"
+  done
+  md_count="$(printf '%s\n' "$md_hits" | wc -l | tr -d ' ')"
+  count=$((count + md_count))
+fi
+
+if [ "$count" -gt 0 ]; then
+  printf 'check-issue-refs: %s hit(s) found\n' "$count" >&2
   exit 1
 fi
 exit 0