Migrate to Viper for unified configuration management (bd-78)

- Add Viper dependency and create internal/config package
- Initialize Viper singleton with config file search paths
- Bind all global flags to Viper with proper precedence (flags > env > config > defaults)
- Replace manual os.Getenv() calls with config.GetString/GetBool/GetDuration
- Update CONFIG.md with comprehensive Viper documentation
- Add comprehensive tests for config precedence and env binding
- Walk up parent directories to discover .beads/config.yaml from subdirectories
- Add env key replacer for hyphenated keys (BD_NO_DAEMON -> no-daemon)
- Remove deprecated prefer-global-daemon setting
- Move Viper config apply before early-return to support version/init/help commands

Hybrid architecture maintains separation:
- Viper: User-specific tool preferences (--json, --no-daemon, etc.)
- bd config: Team-shared project data (Jira URLs, Linear tokens, etc.)

All tests passing. Closes bd-78, bd-79, bd-80, bd-81, bd-82, bd-83.

Amp-Thread-ID: https://ampcode.com/threads/T-0d0f8c1d-b877-4fa9-8477-b6fea63fb664
Co-authored-by: Amp <amp@ampcode.com>

go.mod

@@ -18,17 +18,28 @@ require (
 
 require (
 	github.com/dustin/go-humanize v1.0.1 // indirect
+	github.com/fsnotify/fsnotify v1.9.0 // indirect
+	github.com/go-viper/mapstructure/v2 v2.4.0 // indirect
 	github.com/inconshreveable/mousetrap v1.1.0 // indirect
 	github.com/mattn/go-colorable v0.1.13 // indirect
 	github.com/mattn/go-isatty v0.0.20 // indirect
 	github.com/ncruces/go-strftime v0.1.9 // indirect
+	github.com/pelletier/go-toml/v2 v2.2.4 // indirect
 	github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec // indirect
+	github.com/sagikazarmark/locafero v0.11.0 // indirect
+	github.com/sourcegraph/conc v0.3.1-0.20240121214520-5f936abd7ae8 // indirect
+	github.com/spf13/afero v1.15.0 // indirect
+	github.com/spf13/cast v1.10.0 // indirect
 	github.com/spf13/pflag v1.0.10 // indirect
+	github.com/spf13/viper v1.21.0 // indirect
+	github.com/subosito/gotenv v1.6.0 // indirect
 	github.com/tidwall/gjson v1.18.0 // indirect
 	github.com/tidwall/match v1.1.1 // indirect
 	github.com/tidwall/pretty v1.2.1 // indirect
 	github.com/tidwall/sjson v1.2.5 // indirect
+	go.yaml.in/yaml/v3 v3.0.4 // indirect
 	golang.org/x/exp v0.0.0-20250620022241-b7579e27df2b // indirect
+	golang.org/x/text v0.28.0 // indirect
 	golang.org/x/tools v0.37.0 // indirect
 	modernc.org/libc v1.66.3 // indirect
 	modernc.org/mathutil v1.7.1 // indirect