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debmake-doc 1.17-7
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 $ cd debhello-0.0
 $ dquilt new 000-prefix-usr.patch
Patch debian/patches/000-prefix-usr.patch is now on top
 $ dquilt add Makefile
File Makefile added to patch debian/patches/000-prefix-usr.patch
 ... hack, hack, hack, ...
 $ head -1 Makefile
prefix = /usr
 $ dquilt refresh
Refreshed patch debian/patches/000-prefix-usr.patch
 $ dquilt header -e --dep3
 ... edit the DEP-3 patch header with editor
 $ tree -a
.
├── .pc
│   ├── .quilt_patches
│   ├── .quilt_series
│   ├── .version
│   ├── 000-prefix-usr.patch
│   │   ├── .timestamp
│   │   └── Makefile
│   └── applied-patches
├── LICENSE
├── Makefile
├── debian
│   ├── README.Debian
│   ├── changelog
│   ├── control
│   ├── copyright
│   ├── patches
│   │   ├── 000-prefix-usr.patch
│   │   └── series
│   ├── rules
│   ├── source
│   │   ├── control
│   │   ├── format
│   │   ├── local-options
│   │   ├── options
│   │   └── patch-header
│   ├── tests
│   │   └── control
│   ├── upstream
│   │   └── metadata
│   └── watch
└── src
    └── hello.c

8 directories, 24 files
 $ cat debian/patches/series
000-prefix-usr.patch
 $ cat debian/patches/000-prefix-usr.patch
Description: set prefix=/usr patch
Author: Osamu Aoki <osamu@debian.org>
Index: debhello-0.0/Makefile
===================================================================
--- debhello-0.0.orig/Makefile
+++ debhello-0.0/Makefile
@@ -1,4 +1,4 @@
-prefix = /usr/local
+prefix = /usr

 all: src/hello