Codex refactor update transactions

Codex did this refactor.

Batch update installs, dependency installs, conflict removals, and replacement removals under one update transaction hook boundary, following pacman's sync transaction model.

Remove the unused pdf-extract dependency and refresh related dependency versions.

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "depot"
-version = "0.50.0"
+version = "0.60.0"
 edition = "2024"
 
 [lints.rust]
@@ -19,13 +19,13 @@ static-except-libc = [
 ]
 
 [dependencies]
-anyhow = "1.0.102"
+anyhow = "1.0.103"
 ar = "0.9.0"
 bzip2 = "0.6.1"
 clap = { version = "4.6.0", features = ["derive"] }
 flate2 = "1.1.9"
 git2 = "0.21.0"
-indicatif = "0.18.4"
+indicatif = "0.18.6"
 nix = { version = "0.31.3", features = ["user"] }
 rusqlite = "0.40.1"
 semver = "1.0.28"
@@ -43,22 +43,21 @@ zip = "8.5.0"
 zstd = { version = "0.13.3", features = ["zstdmt"] }
 inquire = "0.9.4"
 md5 = "0.8.0"
-suppaftp = "8.0.4"
+suppaftp = "10.0.0"
 minisign = "0.9.1"
 petgraph = "0.8.3"
 fd-lock = "4.0.4"
 reqwest = { version = "0.13.4", default-features = false, features = ["blocking", "native-tls"] }
 filetime = "0.2.29"
-clap_complete = "4.6.5"
+clap_complete = "4.6.7"
 sys-mount = { version = "3.1.0", default-features = false }
-time = { version = "0.3.49", features = ["formatting", "parsing"] }
+time = { version = "0.3.53", features = ["formatting", "parsing"] }
 b2sum-rust = "0.3.0"
 serde_ignored = "0.1.14"
 lz4_flex = "0.13.1"
-lzma-rust2 = "0.16.4"
+lzma-rust2 = "0.16.5"
 signal-hook = "0.4.4"
 sha1 = "0.11.0"
-pdf-extract = "0.10.0"
 
 [dev-dependencies]
 tempfile = "=3.27.0"