consolidate hardcoded paths into config, refactor apply_agent

Move prompts_dir into Config (was hardcoded ~/poc/memory/prompts).
Replace hardcoded ~/.claude/memory paths in spectral.rs, graph.rs,
and main.rs with store::memory_dir() or config::get(). Replace
hardcoded ~/.claude/projects in knowledge.rs and main.rs with
config::get().projects_dir.

Extract apply_agent_file() from cmd_apply_agent() — separates
file scanning from per-file JSON parsing and link application.

poc-memory/src/spectral.rs

@@ -43,8 +43,7 @@ pub struct SpectralEmbedding {
 }
 
 fn embedding_path() -> PathBuf {
-    let home = std::env::var("HOME").unwrap_or_default();
-    PathBuf::from(home).join(".claude/memory/spectral-embedding.json")
+    crate::store::memory_dir().join("spectral-embedding.json")
 }
 
 /// Compute spectral decomposition of the memory graph.