diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c759f4e..d1c7513 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -123,6 +123,11 @@ jobs:
           echo "Validating tracked shell scripts are executable..."
           ./scripts/check-script-permissions.sh
 
+      - name: Validate skill folders are self-contained
+        run: |
+          echo "Validating no skill symlink escapes its skill folder..."
+          ./scripts/check-skill-links.sh
+
       - name: Validate hooks.json
         run: |
           echo "Validating hooks/hooks.json..."
diff --git a/Makefile b/Makefile
index 6b0d459..2a7a093 100644
--- a/Makefile
+++ b/Makefile
@@ -104,6 +104,8 @@ lint:
 		| xargs shellcheck -x
 	@echo "🔍 Checking script permissions..."
 	@./scripts/check-script-permissions.sh
+	@echo "🔍 Checking skill links..."
+	@./scripts/check-skill-links.sh
 	@echo "🔍 Checking bats assertions..."
 	@./scripts/check-bats-assertions.sh
 	@echo "✅ Lint complete!"
diff --git a/scripts/check-skill-links.sh b/scripts/check-skill-links.sh
new file mode 100755
index 0000000..5fb00bf
--- /dev/null
+++ b/scripts/check-skill-links.sh
@@ -0,0 +1,68 @@
+#!/bin/bash
+
+# Fails if a skill ships a symlink that points outside its own skill folder.
+# Per-skill-dir installers reject escaping paths, so each skill folder stays
+# self-contained. Reads the index rather than the working tree — the index is
+# what a fresh clone gets. Must be run from the repository root.
+
+set -euo pipefail
+
+if ! command -v git >/dev/null 2>&1; then
+    echo "FAIL: git is required to check skill links"
+    exit 1
+fi
+
+if ! git rev-parse --show-toplevel >/dev/null 2>&1; then
+    echo "FAIL: not inside a git repository"
+    exit 1
+fi
+
+failed=0
+count=0
+
+while IFS=$'\t' read -r meta path; do
+    [ -n "$meta" ] || continue
+    mode="${meta%% *}"
+    [ "$mode" = "120000" ] || continue
+    count=$((count + 1))
+
+    skill_dir="$(echo "$path" | cut -d/ -f1-2)"
+    skill_abs="$(cd "$skill_dir" && pwd -P)"
+    if ! target="$(readlink "$path" 2>/dev/null)"; then
+        echo "FAIL: $path is tracked as a symlink but is not one on disk (stage your changes)"
+        failed=1
+        continue
+    fi
+
+    case "$target" in
+        /*) abs="$target" ;;
+        *) abs="$(cd "$(dirname "$path")" && pwd -P)/$target" ;;
+    esac
+
+    if ! dir_canon="$(cd -P "$(dirname "$abs")" 2>/dev/null && pwd)"; then
+        echo "FAIL: $path points at missing location $target"
+        failed=1
+        continue
+    fi
+    canon="$dir_canon/$(basename "$abs")"
+
+    if [ ! -e "$canon" ]; then
+        echo "FAIL: $path points at missing location $target"
+        failed=1
+        continue
+    fi
+
+    case "$canon" in
+        "$skill_abs"/*) ;;
+        *)
+            echo "FAIL: $path escapes $skill_dir (points at $target)"
+            failed=1
+            ;;
+    esac
+done < <(git ls-files -s -- 'skills/*')
+
+if [ "$failed" -eq 1 ]; then
+    exit 1
+fi
+
+echo "PASS: $count skill symlink(s) stay inside their skill folder"
diff --git a/scripts/check-skill-links.test.bats b/scripts/check-skill-links.test.bats
new file mode 100644
index 0000000..a0366ef
--- /dev/null
+++ b/scripts/check-skill-links.test.bats
@@ -0,0 +1,94 @@
+#!/usr/bin/env bats
+
+# Unit Tests for scripts/check-skill-links.sh
+# All tests invoke as subprocess against temp fixture git repositories
+
+PROJECT_ROOT="$(cd "$(dirname "$BATS_TEST_FILENAME")/.." && pwd)"
+export PROJECT_ROOT
+
+load "$PROJECT_ROOT/tests/helpers/assertions.bash"
+
+LINKS_SCRIPT="$PROJECT_ROOT/scripts/check-skill-links.sh"
+
+setup() {
+    FIXTURE_DIR="$(mktemp -d)"
+
+    # Build a fixture repo with one self-contained skill
+    mkdir -p "$FIXTURE_DIR/skills/demo/scripts"
+    cp "$LINKS_SCRIPT" "$FIXTURE_DIR/scripts-check-skill-links.sh"
+    printf '#!/bin/bash\necho ok\n' > "$FIXTURE_DIR/skills/demo/scripts/gate.sh"
+    printf '# Skill\n' > "$FIXTURE_DIR/skills/demo/SKILL.md"
+
+    cd "$FIXTURE_DIR"
+    git init -q .
+    git add -A
+}
+
+teardown() {
+    rm -rf "$FIXTURE_DIR"
+}
+
+run_links_script() {
+    run bash "$FIXTURE_DIR/scripts-check-skill-links.sh"
+}
+
+# --- Happy path ---
+
+@test "check-skill-links passes when a skill has no symlinks" {
+    cd "$FIXTURE_DIR"
+    run_links_script
+    [ "$status" -eq 0 ]
+    assert_output_contains "PASS: 0 skill symlink(s) stay inside their skill folder"
+}
+
+@test "check-skill-links passes when a link stays inside its skill folder" {
+    cd "$FIXTURE_DIR"
+    ln -sf gate.sh "$FIXTURE_DIR/skills/demo/scripts/inner.sh"
+    git add -A
+    run_links_script
+    [ "$status" -eq 0 ]
+    assert_output_contains "PASS: 1 skill symlink(s)"
+}
+
+# --- Escaping links ---
+
+@test "check-skill-links fails and names a link pointing outside its skill folder" {
+    cd "$FIXTURE_DIR"
+    mkdir -p shared
+    printf '#!/bin/bash\n' > shared/gate.sh
+    ln -sf ../../../shared/gate.sh "$FIXTURE_DIR/skills/demo/scripts/gate.sh"
+    git add -A
+    run_links_script
+    [ "$status" -eq 1 ]
+    assert_output_contains "skills/demo/scripts/gate.sh escapes skills/demo"
+}
+
+@test "check-skill-links fails on an absolute link target" {
+    cd "$FIXTURE_DIR"
+    ln -sf /bin/sh "$FIXTURE_DIR/skills/demo/scripts/gate.sh"
+    git add -A
+    run_links_script
+    [ "$status" -eq 1 ]
+    assert_output_contains "escapes skills/demo"
+}
+
+@test "check-skill-links fails on a dangling link" {
+    cd "$FIXTURE_DIR"
+    ln -sf nowhere.sh "$FIXTURE_DIR/skills/demo/scripts/gate.sh"
+    git add -A
+    run_links_script
+    [ "$status" -eq 1 ]
+    assert_output_contains "points at missing location"
+}
+
+@test "check-skill-links checks each skill against its own folder" {
+    cd "$FIXTURE_DIR"
+    mkdir -p "$FIXTURE_DIR/skills/other/scripts"
+    printf '# Skill\n' > "$FIXTURE_DIR/skills/other/SKILL.md"
+    printf '#!/bin/bash\n' > "$FIXTURE_DIR/skills/other/scripts/gate.sh"
+    ln -sf ../../demo/scripts/gate.sh "$FIXTURE_DIR/skills/other/scripts/gate.sh"
+    git add -A
+    run_links_script
+    [ "$status" -eq 1 ]
+    assert_output_contains "skills/other/scripts/gate.sh escapes skills/other"
+}
diff --git a/skills/document/scripts/doc-gates.sh b/skills/document/scripts/doc-gates.sh
deleted file mode 120000
index 88f79bd..0000000
--- a/skills/document/scripts/doc-gates.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../scripts/doc-gates.sh
\ No newline at end of file
diff --git a/skills/document/scripts/doc-gates.sh b/skills/document/scripts/doc-gates.sh
new file mode 100755
index 0000000..2efda24
--- /dev/null
+++ b/skills/document/scripts/doc-gates.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+# Document skill gates - checks agent output before the next batch
+# Usage: doc-gates.sh <analysis|generation> [sf-dir]
+
+MODE="$1"
+case "$MODE" in
+    analysis) FILES="artifacts-summary.md implementation-summary.md docs-inventory.md" ;;
+    generation) FILES="technical-docs.md user-docs.md" ;;
+    *) echo "Usage: doc-gates.sh <analysis|generation> [sf-dir]" >&2; exit 1 ;;
+esac
+
+RESEARCH="${2:-${SF_DIR:-.sf}}/research"
+
+# A marker shape means an unfinished draft. A bare word like "placeholder" in a
+# props table is ordinary prose.
+MARKER='(TODO|TBD)[[:space:]]*:|[[<](TODO|TBD|PLACEHOLDER|INSERT)'
+
+# An inline code span quotes a marker, it does not leave one, so strip spans first.
+has_marker() {
+    # shellcheck disable=SC2016  # the backticks are markdown, not a subshell
+    sed 's/`[^`]*`//g' "$1" | grep -qiE "$MARKER"
+}
+
+STATUS=0
+for file in $FILES; do
+    if [ ! -f "$RESEARCH/$file" ]; then
+        echo "FAIL $file: missing from $RESEARCH" >&2
+        STATUS=1
+    # An empty file is a valid "no docs needed" signal. Only markers fail.
+    elif [ "$MODE" = generation ] && has_marker "$RESEARCH/$file"; then
+        echo "FAIL $file: contains a placeholder marker" >&2
+        STATUS=1
+    else
+        echo "PASS $file"
+    fi
+done
+exit $STATUS
diff --git a/skills/implement/scripts/validate-implementation.sh b/skills/implement/scripts/validate-implementation.sh
deleted file mode 120000
index 13185f6..0000000
--- a/skills/implement/scripts/validate-implementation.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../scripts/validate-implementation.sh
\ No newline at end of file
diff --git a/skills/implement/scripts/validate-implementation.sh b/skills/implement/scripts/validate-implementation.sh
new file mode 100755
index 0000000..c2a3aa5
--- /dev/null
+++ b/skills/implement/scripts/validate-implementation.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+# Implementation check - counts the acceptance criteria the spec still has unchecked
+# Usage: validate-implementation.sh [sf-dir]
+
+SF_DIR="${1:-${SF_DIR:-.sf}}"
+SPEC_FILE="$SF_DIR/spec.md"
+IMPL_FILE="$SF_DIR/implementation-summary.md"
+
+# Before both files exist there is nothing to compare.
+if [ ! -f "$SPEC_FILE" ] || [ ! -f "$IMPL_FILE" ]; then exit 0; fi
+
+CRITERIA=$(grep -i "^\- \[" "$SPEC_FILE" 2>/dev/null)
+[ -z "$CRITERIA" ] && exit 0
+
+UNCHECKED=$(echo "$CRITERIA" | grep -c "^\- \[ \]")
+if [ "$UNCHECKED" -gt 0 ]; then
+    echo "$UNCHECKED acceptance criteria unchecked in spec" >&2
+    exit 1
+fi
+exit 0
diff --git a/skills/spec/scripts/spec-dir.sh b/skills/spec/scripts/spec-dir.sh
deleted file mode 120000
index a8b10e7..0000000
--- a/skills/spec/scripts/spec-dir.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../scripts/spec-dir.sh
\ No newline at end of file
diff --git a/skills/spec/scripts/spec-dir.sh b/skills/spec/scripts/spec-dir.sh
new file mode 100755
index 0000000..77296ac
--- /dev/null
+++ b/skills/spec/scripts/spec-dir.sh
@@ -0,0 +1,60 @@
+#!/bin/bash
+# SF artifact directory setup - prepares $SF_DIR for a spec run
+# Usage: spec-dir.sh <first|update|new> [sf-dir]
+
+MODE="$1"
+case "$MODE" in
+    first|update|new) ;;
+    *) echo "Usage: spec-dir.sh <first|update|new> [sf-dir]" >&2; exit 1 ;;
+esac
+
+# Resolve the artifact directory: argument, then $SF_DIR, then a marker walk
+SF_DIR="${2:-$SF_DIR}"
+if [ -z "$SF_DIR" ]; then
+    PROJECT_ROOT="$(pwd)"
+    while [ ! -e "$PROJECT_ROOT/.git" ] && [ ! -f "$PROJECT_ROOT/AGENTS.md" ] && [ ! -f "$PROJECT_ROOT/CLAUDE.md" ]; do
+        [ "$PROJECT_ROOT" = "/" ] && { echo "Error: project root not found. Looked for .git, AGENTS.md or CLAUDE.md in $(pwd) and every parent directory." >&2; exit 1; }
+        PROJECT_ROOT="$(dirname "$PROJECT_ROOT")"
+    done
+    SF_DIR="$PROJECT_ROOT/.sf"
+    [ -d "$PROJECT_ROOT/.git" ] && [ -f "$PROJECT_ROOT/.gitignore" ] && ! grep -qF '.sf/' "$PROJECT_ROOT/.gitignore" && echo '.sf/' >> "$PROJECT_ROOT/.gitignore"
+fi
+
+mkdir -p "$SF_DIR" 2>/dev/null || { echo "Error: Cannot create or write to $SF_DIR" >&2; exit 1; }
+
+case "$MODE" in
+    "update")
+        cp "$SF_DIR/spec.md" "$SF_DIR/spec-backup.md" 2>/dev/null
+        # No trailing slash: this must remove a symlink as a symlink
+        rm -rf "$SF_DIR/research"
+        ;;
+    "new")
+        # Never reuse an archive name, even for two runs in the same second
+        name=$(date -u +%Y-%m-%dT%H%M%S)
+        suffix=1
+        while [ -e "$SF_DIR/specs/$name" ]; do
+            name="$(date -u +%Y-%m-%dT%H%M%S)-$suffix"
+            suffix=$((suffix + 1))
+        done
+        mkdir -p "$SF_DIR/specs/$name"
+        # A symlink already points into an older archive. Drop it and keep that archive.
+        if [ -L "$SF_DIR/spec.md" ]; then
+            rm -f "$SF_DIR/spec.md"
+        else
+            mv "$SF_DIR/spec.md" "$SF_DIR/specs/$name/" 2>/dev/null
+        fi
+        if [ -L "$SF_DIR/research" ]; then
+            rm -f "$SF_DIR/research"
+        else
+            mv "$SF_DIR/research" "$SF_DIR/specs/$name/" 2>/dev/null
+        fi
+        mkdir -p "$SF_DIR/specs/$name/research"
+        if ! ln -sfn "specs/$name/spec.md" "$SF_DIR/spec.md" || ! ln -sfn "specs/$name/research" "$SF_DIR/research"; then
+            rm -rf "$SF_DIR/specs/$name/"
+            echo "Error: Failed to create symlinks" >&2
+            exit 1
+        fi
+        ;;
+esac
+
+mkdir -p "$SF_DIR/research"
diff --git a/skills/spec/scripts/validate-spec.sh b/skills/spec/scripts/validate-spec.sh
deleted file mode 120000
index c92500b..0000000
--- a/skills/spec/scripts/validate-spec.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../scripts/validate-spec.sh
\ No newline at end of file
diff --git a/skills/spec/scripts/validate-spec.sh b/skills/spec/scripts/validate-spec.sh
new file mode 100755
index 0000000..4575b0c
--- /dev/null
+++ b/skills/spec/scripts/validate-spec.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+# Spec structure check - reports the sections spec.md does not have
+# Usage: validate-spec.sh [sf-dir]
+
+SPEC_FILE="${1:-${SF_DIR:-.sf}}/spec.md"
+
+# No spec yet means nothing to check.
+[ ! -f "$SPEC_FILE" ] && exit 0
+
+MISSING=""
+grep -qi "scope\|problem" "$SPEC_FILE" || MISSING="$MISSING scope/problem,"
+grep -qi "criteria\|acceptance" "$SPEC_FILE" || MISSING="$MISSING acceptance criteria,"
+grep -qi "risk" "$SPEC_FILE" || MISSING="$MISSING risks,"
+
+if [ -n "$MISSING" ]; then
+    echo "Spec missing sections:${MISSING%,}" >&2
+    exit 1
+fi
+exit 0