chore: rename packages/ to crates/

Move all 29 workspace members from packages/<name>/ to crates/<name>/.
Updates: workspace Cargo.toml (members + path deps), justfile, root
CLAUDE.md, scripts/build/CARGO_INSTALL.md, docs/architecture/crates.md
(renamed from packages.md), structural references in docs/architecture
and docs/configuration, per-crate CLAUDE.md self-references. Historical
plans, reports, and building/ docs are left untouched.

No behavior change; just check-all stays green and fermata tests pass.

Cargo.toml

@@ -0,0 +1,37 @@
+[package]
+name = "dirigent_fermata"
+version = "0.1.0"
+edition = "2021"
+description = "Harness-agnostic policy gate for AI coding agents (.botignore + botignore.toml)"
+
+[lib]
+path = "src/lib.rs"
+
+[[bin]]
+name = "fermata"
+path = "src/bin/fermata.rs"
+required-features = ["cli"]
+
+[dependencies]
+globset = "0.4"
+ignore = "0.4"
+walkdir = "2"
+toml = "0.8"
+regex = "1.10"
+serde = { version = "1.0", features = ["derive"] }
+serde_json = "1.0"
+thiserror = "2.0"
+clap = { version = "4.5", features = ["derive"], optional = true }
+
+[dev-dependencies]
+tempfile = "3.10"
+assert_cmd = "2.0"
+predicates = "3.1"
+
+[features]
+default = ["cli", "harness-claude"]
+cli = ["dep:clap"]
+harness-claude = []
+
+[lints]
+workspace = true