Clean up project for initial release

.clojure-skills/config.edn

@@ -0,0 +1,12 @@
+{:database {:path "~/dev/clojure-skills/clojure-skills.db",
+            :auto-migrate true},
+ :project {:root nil,
+           :skills-dir "skills",
+           :prompts-dir "prompts",
+           :build-dir "_build"},
+
+ :permissions
+ {:prompt    true}
+
+ :search {:max-results 50, :context-lines 3},
+ :output {:format :table, :color true}}

deps.edn

@@ -10,7 +10,7 @@
   org.clj-commons/pretty {:mvn/version "3.6.7"}
   dev.weavejester/hashp {:mvn/version "0.5.1"}
   io.github.paintparty/bling {:mvn/version "0.8.8"}
-  dev.glossa/metazoa {:mvn/version "0.2.298"}
+
   mvxcvi/puget {:mvn/version "1.3.4"}
 
   ;; SQL database dependencies
@@ -26,6 +26,7 @@
 
  :aliases {:dev {:extra-deps
                  {vvvvalvalval/scope-capture {:mvn/version "0.3.3"}
+                  dev.glossa/metazoa {:mvn/version "0.2.298"}
                   org.clojure/tools.nrepl {:mvn/version "0.2.11"}
                   nubank/matcher-combinators {:mvn/version "3.9.1"}
                   com.stuartsierra/component.repl {:mvn/version "0.2.0"}

prompt_configs/clojure_build.yaml

@@ -15,6 +15,6 @@ fragments:
   - skills/libraries/metadata/metazoa.md
   - skills/tooling/hashp.md
   - skills/libraries/logging/pretty.md
-  - skills/tooling/clojure_lsp_api
+  - skills/tooling/clojure_lsp_api.md
   - skills/tooling/clj_paren_repair.md
 references: []

prompt_configs/clojure_skill_builder.yaml

@@ -13,9 +13,7 @@ fragments:
   - skills/libraries/metadata/metazoa.md
   - skills/tooling/hashp.md
   - skills/libraries/logging/pretty.md
-  - skills/tooling/clojure_lsp_api
+  - skills/tooling/clojure_lsp_api.md
   - skills/tooling/clj_paren_repair.md
   - skills/tooling/clojure_mcp_light.md
-  - skills/libraries/data_formats/pretty.md
-
-  references: []
+references: []

resources/migrations/001-initial-schema.edn

@@ -3,6 +3,7 @@
  :up
  ["PRAGMA foreign_keys = ON"
 
+  ;; Skills table
   "CREATE TABLE IF NOT EXISTS skills (
      id INTEGER PRIMARY KEY AUTOINCREMENT,
      path TEXT NOT NULL UNIQUE,
@@ -22,6 +23,7 @@
   "CREATE INDEX IF NOT EXISTS idx_skills_name ON skills(name)"
   "CREATE INDEX IF NOT EXISTS idx_skills_hash ON skills(file_hash)"
 
+  ;; Prompts table (includes fragment_refs column from migration 006)
   "CREATE TABLE IF NOT EXISTS prompts (
      id INTEGER PRIMARY KEY AUTOINCREMENT,
      path TEXT NOT NULL UNIQUE,
@@ -33,25 +35,65 @@
      file_hash TEXT NOT NULL,
      size_bytes INTEGER NOT NULL,
      token_count INTEGER,
+     fragment_refs TEXT,
      created_at TEXT NOT NULL DEFAULT (datetime('now')),
      updated_at TEXT NOT NULL DEFAULT (datetime('now'))
    )"
 
-  "CREATE INDEX IF NOT EXISTS idx_prompts_name ON prompts(name)"
   "CREATE INDEX IF NOT EXISTS idx_prompts_hash ON prompts(file_hash)"
+  ;; Unique index on name (from migration 008)
+  "CREATE UNIQUE INDEX IF NOT EXISTS idx_prompts_name ON prompts(name)"
 
-  "CREATE TABLE IF NOT EXISTS prompt_skills (
-     prompt_id INTEGER NOT NULL,
+  ;; Prompt fragments table (from migration 006)
+  "CREATE TABLE IF NOT EXISTS prompt_fragments (
+     id INTEGER PRIMARY KEY AUTOINCREMENT,
+     name TEXT NOT NULL UNIQUE,
+     title TEXT,
+     description TEXT,
+     created_at TEXT NOT NULL DEFAULT (datetime('now')),
+     updated_at TEXT NOT NULL DEFAULT (datetime('now'))
+   )"
+
+  "CREATE INDEX IF NOT EXISTS idx_prompt_fragments_name ON prompt_fragments(name)"
+
+  ;; Prompt fragment skills join table (from migration 006)
+  "CREATE TABLE IF NOT EXISTS prompt_fragment_skills (
+     fragment_id INTEGER NOT NULL,
      skill_id INTEGER NOT NULL,
      position INTEGER NOT NULL,
-     PRIMARY KEY (prompt_id, skill_id),
-     FOREIGN KEY (prompt_id) REFERENCES prompts(id) ON DELETE CASCADE,
+     created_at TEXT NOT NULL DEFAULT (datetime('now')),
+     PRIMARY KEY (fragment_id, skill_id),
+     FOREIGN KEY (fragment_id) REFERENCES prompt_fragments(id) ON DELETE CASCADE,
      FOREIGN KEY (skill_id) REFERENCES skills(id) ON DELETE CASCADE
    )"
 
-  "CREATE INDEX IF NOT EXISTS idx_prompt_skills_prompt ON prompt_skills(prompt_id)"
-  "CREATE INDEX IF NOT EXISTS idx_prompt_skills_skill ON prompt_skills(skill_id)"
+  "CREATE INDEX IF NOT EXISTS idx_prompt_fragment_skills_fragment ON prompt_fragment_skills(fragment_id)"
+  "CREATE INDEX IF NOT EXISTS idx_prompt_fragment_skills_skill ON prompt_fragment_skills(skill_id)"
 
+  ;; Prompt references table (from migration 006, with FIXED nullable target_prompt_id)
+  "CREATE TABLE IF NOT EXISTS prompt_references (
+     id INTEGER PRIMARY KEY AUTOINCREMENT,
+     source_prompt_id INTEGER NOT NULL,
+     target_prompt_id INTEGER,
+     target_fragment_id INTEGER,
+     reference_type TEXT NOT NULL CHECK(reference_type IN ('prompt', 'fragment')),
+     position INTEGER NOT NULL,
+     created_at TEXT NOT NULL DEFAULT (datetime('now')),
+     FOREIGN KEY (source_prompt_id) REFERENCES prompts(id) ON DELETE CASCADE,
+     FOREIGN KEY (target_prompt_id) REFERENCES prompts(id) ON DELETE CASCADE,
+     FOREIGN KEY (target_fragment_id) REFERENCES prompt_fragments(id) ON DELETE CASCADE,
+     CONSTRAINT chk_target_reference CHECK (
+       (target_prompt_id IS NOT NULL AND target_fragment_id IS NULL) OR
+       (target_prompt_id IS NULL AND target_fragment_id IS NOT NULL)
+     )
+   )"
+
+  "CREATE INDEX IF NOT EXISTS idx_prompt_references_source ON prompt_references(source_prompt_id)"
+  "CREATE INDEX IF NOT EXISTS idx_prompt_references_target_prompt ON prompt_references(target_prompt_id)"
+  "CREATE INDEX IF NOT EXISTS idx_prompt_references_target_fragment ON prompt_references(target_fragment_id)"
+  "CREATE INDEX IF NOT EXISTS idx_prompt_references_type ON prompt_references(reference_type)"
+
+  ;; Skills FTS table
   "CREATE VIRTUAL TABLE IF NOT EXISTS skills_fts USING fts5(
      path,
      category,
@@ -63,6 +105,7 @@
      content_rowid='id'
    )"
 
+  ;; Skills FTS triggers
   "CREATE TRIGGER IF NOT EXISTS skills_ai AFTER INSERT ON skills BEGIN
      INSERT INTO skills_fts(rowid, path, category, name, title, description, content)
      VALUES (new.id, new.path, new.category, new.name, new.title, new.description, new.content);
@@ -80,6 +123,7 @@
      VALUES (new.id, new.path, new.category, new.name, new.title, new.description, new.content);
    END"
 
+  ;; Prompts FTS table
   "CREATE VIRTUAL TABLE IF NOT EXISTS prompts_fts USING fts5(
      path,
      name,
@@ -91,6 +135,7 @@
      content_rowid='id'
    )"
 
+  ;; Prompts FTS triggers
   "CREATE TRIGGER IF NOT EXISTS prompts_ai AFTER INSERT ON prompts BEGIN
      INSERT INTO prompts_fts(rowid, path, name, title, author, description, content)
      VALUES (new.id, new.path, new.name, new.title, new.author, new.description, new.content);
@@ -117,11 +162,18 @@
   "DROP TRIGGER IF EXISTS skills_ad"
   "DROP TRIGGER IF EXISTS skills_ai"
   "DROP TABLE IF EXISTS skills_fts"
-  "DROP INDEX IF EXISTS idx_prompt_skills_skill"
-  "DROP INDEX IF EXISTS idx_prompt_skills_prompt"
-  "DROP TABLE IF EXISTS prompt_skills"
-  "DROP INDEX IF EXISTS idx_prompts_hash"
+  "DROP INDEX IF EXISTS idx_prompt_references_type"
+  "DROP INDEX IF EXISTS idx_prompt_references_target_fragment"
+  "DROP INDEX IF EXISTS idx_prompt_references_target_prompt"
+  "DROP INDEX IF EXISTS idx_prompt_references_source"
+  "DROP TABLE IF EXISTS prompt_references"
+  "DROP INDEX IF EXISTS idx_prompt_fragment_skills_skill"
+  "DROP INDEX IF EXISTS idx_prompt_fragment_skills_fragment"
+  "DROP TABLE IF EXISTS prompt_fragment_skills"
+  "DROP INDEX IF EXISTS idx_prompt_fragments_name"
+  "DROP TABLE IF EXISTS prompt_fragments"
   "DROP INDEX IF EXISTS idx_prompts_name"
+  "DROP INDEX IF EXISTS idx_prompts_hash"
   "DROP TABLE IF EXISTS prompts"
   "DROP INDEX IF EXISTS idx_skills_hash"
   "DROP INDEX IF EXISTS idx_skills_name"

src/clojure_skills/config.clj

@@ -106,10 +106,7 @@
     :color  true}
 
    :permissions
-   {:plan      false
-    :task      false
-    :task-list false
-    :prompt    false}})
+   {:prompt    false}})
 
 (defn get-config-file-path
   "Get path to config.edn file."

src/clojure_skills/db/prompt_fragments.clj

@@ -183,17 +183,25 @@
 
     ;; Note: Using raw SQL for INSERT...RETURNING because HoneySQL has issues
     ;; with SQLite's RETURNING clause
-    (jdbc/execute-one!
-     db
-     ["INSERT INTO prompt_references 
-       (source_prompt_id, target_prompt_id, target_fragment_id, reference_type, position)
-       VALUES (?, ?, ?, ?, ?)
-       RETURNING *"
-      (:source_prompt_id reference-map)
-      (:target_prompt_id reference-map)
-      (:target_fragment_id reference-map)
-      (:reference_type reference-map)
-      (:position reference-map)])))
+    ;; Build SQL dynamically based on which target is provided
+    (let [has-target-prompt (some? (:target_prompt_id reference-map))
+          columns (if has-target-prompt
+                    "source_prompt_id, target_prompt_id, reference_type, position"
+                    "source_prompt_id, target_fragment_id, reference_type, position")
+          placeholders (if has-target-prompt "?, ?, ?, ?" "?, ?, ?, ?")
+          values (if has-target-prompt
+                   [(:source_prompt_id reference-map)
+                    (:target_prompt_id reference-map)
+                    (:reference_type reference-map)
+                    (:position reference-map)]
+                   [(:source_prompt_id reference-map)
+                    (:target_fragment_id reference-map)
+                    (:reference_type reference-map)
+                    (:position reference-map)])]
+      (jdbc/execute-one!
+       db
+       (into [(str "INSERT INTO prompt_references (" columns ") VALUES (" placeholders ") RETURNING *")]
+             values)))))
 
 (defn get-references-for-prompt
   "Get all references for a specific prompt, ordered by position."

tests.edn

@@ -0,0 +1,9 @@
+#kaocha/v1
+{:tests      [{:id           :unit
+               :test-paths   ["test"]
+               :source-paths ["src"]}]
+ :plugins    [:kaocha.plugin/profiling
+              :kaocha.plugin/junit-xml]
+ :reporter   [kaocha.report/documentation]
+ :color?     false
+ :fail-fast? false}