Issue 1:
After running make.bash standard packages are not installed, I need to run go install std to install them:

~/src/go/src$ git status
# On branch master
# Your branch is up-to-date with 'origin/master'.
#
nothing to commit, working directory clean

~/src/go/src$ env | grep GO
GOROOT=/usr/local/google/home/dvyukov/src/go/src/..
GOPATH=/usr/local/google/home/dvyukov/src/gopath

~/src/go/src$ ./make.bash
##### Building Go bootstrap tool.
cmd/dist

##### Building Go toolchain using /usr/local/google/home/dvyukov/go1.4.
bootstrap/internal/obj
bootstrap/asm/internal/flags
bootstrap/compile/internal/big
bootstrap/internal/gcprog
bootstrap/internal/obj/arm
bootstrap/internal/obj/arm64
bootstrap/internal/obj/ppc64
bootstrap/internal/obj/x86
bootstrap/asm/internal/lex
bootstrap/link/internal/ld
bootstrap/compile/internal/gc
bootstrap/asm/internal/arch
bootstrap/asm/internal/asm
bootstrap/asm
bootstrap/link/internal/amd64
bootstrap/link/internal/arm
bootstrap/link/internal/arm64
bootstrap/link/internal/ppc64
bootstrap/link/internal/x86
bootstrap/link
bootstrap/compile/internal/amd64
bootstrap/compile/internal/arm
bootstrap/compile/internal/arm64
bootstrap/compile/internal/ppc64
bootstrap/compile/internal/x86
bootstrap/compile

##### Building go_bootstrap for host, linux/amd64.
runtime
errors
sync/atomic
sync
internal/singleflight
io
unicode
unicode/utf8
unicode/utf16
bytes
math
strings
strconv
bufio
sort
container/heap
encoding/base64
syscall
internal/syscall/windows/registry
time
internal/syscall/windows
os
reflect
fmt
encoding
encoding/binary
encoding/json
flag
path/filepath
path
io/ioutil
log
regexp/syntax
regexp
go/token
go/scanner
go/ast
go/parser
os/exec
os/signal
net/url
text/template/parse
text/template
go/doc
go/build
hash
crypto
crypto/sha1
debug/dwarf
debug/elf
cmd/go

##### Building packages and commands for linux/amd64.
runtime
sync/atomic
unicode
errors
unicode/utf8
math
sort
container/list
container/ring
crypto/subtle
encoding
image/color
unicode/utf16
runtime/race
cmd/vet/whitelist
sync
container/heap
image/color/palette
io
internal/singleflight
syscall
hash
crypto/cipher
runtime/trace
hash/crc32
hash/adler32
crypto/hmac
hash/crc64
hash/fnv
bytes
strings
bufio
text/tabwriter
path
html
strconv
math/rand
math/cmplx
time
internal/syscall/unix
compress/bzip2
reflect
regexp/syntax
crypto
crypto/aes
crypto/rc4
encoding/base64
encoding/ascii85
encoding/base32
image
crypto/sha512
crypto/md5
crypto/sha1
crypto/sha256
encoding/pem
os
image/internal/imageutil
image/draw
image/jpeg
regexp
os/signal
path/filepath
io/ioutil
os/exec
encoding/binary
fmt
cmd/pprof/internal/svg
crypto/des
index/suffixarray
cmd/internal/rsc.io/x86/x86asm
log
cmd/internal/rsc.io/arm/armasm
debug/gosym
flag
debug/dwarf
debug/plan9obj
archive/tar
compress/flate
compress/lzw
math/big
encoding/hex
go/token
database/sql/driver
encoding/csv
encoding/gob
encoding/json
mime
encoding/xml
mime/quotedprintable
net/http/internal
net/url
text/template/parse
text/scanner
runtime/pprof
internal/trace
net/internal/socktest
runtime/debug
cmd/compile/internal/big
cmd/internal/gcprog
cmd/pprof/internal/tempfile
testing/iotest
cmd/pack
go/scanner
image/gif
database/sql
cmd/internal/obj
testing/quick
cmd/asm/internal/flags
cmd/dist
go/ast
testing
archive/zip
compress/gzip
compress/zlib
image/png
text/template
cmd/pprof/internal/profile
internal/testenv
crypto/elliptic
encoding/asn1
crypto/dsa
crypto/rand
go/constant
debug/elf
debug/macho
debug/pe
cmd/internal/obj/ppc64
cmd/internal/obj/arm64
cmd/internal/obj/arm
cmd/internal/goobj
cmd/internal/obj/x86
cmd/asm/internal/lex
cmd/compile/internal/gc
go/parser
go/printer
crypto/rsa
crypto/x509/pkix
crypto/ecdsa
html/template
go/doc
cmd/internal/objfile
cmd/link/internal/ld
cmd/pprof/internal/plugin
cmd/pprof/internal/symbolz
cmd/pprof/internal/symbolizer
go/types
cmd/cgo
internal/format
cmd/addr2line
cmd/nm
cmd/objdump
cmd/asm/internal/arch
go/build
go/format
cmd/gofmt
cmd/fix
cmd/yacc
cmd/pprof/internal/report
cmd/asm/internal/asm
cmd/cover
cmd/doc
cmd/newlink
cmd/asm
cmd/pprof/internal/commands
cmd/pprof/internal/driver
go/internal/gccgoimporter
go/internal/gcimporter
cmd/api
cmd/link/internal/amd64
cmd/link/internal/arm
cmd/link/internal/arm64
cmd/link/internal/ppc64
cmd/link/internal/x86
runtime/cgo
go/importer
cmd/vet
cmd/link
net
os/user
crypto/x509
net/textproto
log/syslog
mime/multipart
net/mail
crypto/tls
cmd/compile/internal/amd64
cmd/compile/internal/arm
cmd/compile/internal/arm64
cmd/compile/internal/ppc64
cmd/compile/internal/x86
net/http
net/smtp
cmd/compile
net/http/cgi
expvar
net/http/cookiejar
net/http/httptest
net/http/httputil
net/http/pprof
net/rpc
cmd/go
cmd/pprof/internal/fetch
cmd/trace
cmd/pprof
net/http/fcgi
net/rpc/jsonrpc

---
Installed Go for linux/amd64 in /usr/local/google/home/dvyukov/src/go
Installed commands in /usr/local/google/home/dvyukov/src/go/bin

~/src/go/src$ go install -v std
runtime
sync/atomic
unicode
errors
unicode/utf8
math
sort
container/list
container/ring
crypto/subtle
encoding
unicode/utf16
image/color
runtime/race
sync
container/heap
image/color/palette
io
syscall
internal/singleflight
crypto/cipher
hash
runtime/trace
hash/crc32
hash/adler32
crypto/hmac
hash/crc64
hash/fnv
bytes
strings
strconv
math/rand
math/cmplx
bufio
text/tabwriter
path
html
time
internal/syscall/unix
compress/bzip2
reflect
crypto
crypto/aes
crypto/rc4
encoding/base64
encoding/ascii85
encoding/base32
regexp/syntax
image
crypto/md5
crypto/sha512
crypto/sha1
crypto/sha256
encoding/pem
os
image/internal/imageutil
image/draw
image/jpeg
regexp
path/filepath
os/signal
fmt
encoding/binary
io/ioutil
os/exec
crypto/des
index/suffixarray
compress/flate
compress/lzw
archive/tar
math/big
encoding/hex
debug/dwarf
flag
go/token
database/sql/driver
debug/gosym
debug/plan9obj
encoding/csv
encoding/gob
encoding/json
encoding/xml
log
mime
mime/quotedprintable
net/http/internal
net/url
text/template/parse
text/scanner
runtime/pprof
internal/trace
net/internal/socktest
runtime/debug
image/gif
go/scanner
database/sql
testing/iotest
testing/quick
testing
go/ast
archive/zip
compress/gzip
compress/zlib
image/png
text/template
internal/testenv
debug/elf
debug/pe
debug/macho
crypto/dsa
encoding/asn1
crypto/elliptic
crypto/rand
go/constant
go/parser
go/printer
crypto/rsa
crypto/ecdsa
crypto/x509/pkix
go/doc
html/template
go/types
runtime/cgo
internal/format
go/format
go/build
net
os/user
go/internal/gccgoimporter
go/internal/gcimporter
go/importer
crypto/x509
net/textproto
log/syslog
mime/multipart
net/mail
crypto/tls
net/http
net/smtp
expvar
net/http/cgi
net/http/cookiejar
net/http/httptest
net/http/httputil
net/http/pprof
net/rpc
net/http/fcgi
net/rpc/jsonrpc

~/src/go/src$ go install -v std

~/src/go/src$ go version
go version devel +e3c26b2 Mon Aug 3 16:06:52 2015 +0000 linux/amd64

Issue 2:
One symptom:

The behavior of GOROOT_BOOTSTRAP=$HOME/go1.5-bootstrap ./make.bash and

GOROOT_BOOTSTRAP=$HOME/go1.5-bootstrap/ ./make.bash are vastly different

even though the only difference is just a trailing slash added to GOROOT.

($HOME/go1.5-bootstrap is a Go 1.5 installation)

The first will not rebuild std in $GOROOT_BOOTSTRAP, however, the later will.

An easier repro:

$ goroot=`go env GOROOT`
$ cd $goroot/src; ./make.bash # a fresh build
$ GOROOT=$goroot go build -v ../test/helloworld.go # it only build helloworld.go
$ GOROOT=$goroot/ go build -v ../test/helloworld.go # it will recompile runtime

This behavior suggests that some paths that get included in the buildid hash

are not properly Cleaned.